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Interactive post-translational modifications of SRSF, ELAVL and HNRNP proteins.
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Figure 2.html
This file has been truncated, but you can view the full file.
<h2> Instructions </h2>
<h3>Use this plot to browse post-translational modifications from Uniprot.</h3>
<br>
<p>
The buttons at the bottom left allow viewport scaling.
Use the magnifying glass to zoom, the arrows to pan and the home button to return to the original view.
</p>
<p>
Mouse over modifications and domains to see their descriptions.
The bottom-right indicates the 0-based amino-acid position of the mouse pointer.
</p>
<p>
Click on a modification to open a new page with PubMed articles describing that modification
</p>
<style>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"><link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
.legend-box {
cursor: pointer;
}
</style>
<div id="fig_el320884549039056450069957"></div>
<script>
function mpld3_load_lib(url, callback){
var s = document.createElement('script');
s.src = url;
s.async = true;
s.onreadystatechange = s.onload = callback;
s.onerror = function(){console.warn("failed to load library " + url);};
document.getElementsByTagName("head")[0].appendChild(s);
}
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// already loaded: just create the figure
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mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
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obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
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tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
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}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
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tooltip.html(labels[i])
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} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
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tooltip
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.style("left",d3.event.pageX + this.props.hoffset + "px");
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.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("clickablehtmltooltip", PointClickableHTMLTooltip);
PointClickableHTMLTooltip.prototype = Object.create(mpld3.Plugin.prototype);
PointClickableHTMLTooltip.prototype.constructor = PointClickableHTMLTooltip;
PointClickableHTMLTooltip.prototype.requiredProps = ["id"];
PointClickableHTMLTooltip.prototype.defaultProps = {labels:null,
targets:null,
hoffset:0,
voffset:10};
function PointClickableHTMLTooltip(fig, props){
mpld3.Plugin.call(this, fig, props);
};
PointClickableHTMLTooltip.prototype.draw = function(){
var obj = mpld3.get_element(this.props.id);
var labels = this.props.labels;
var targets = this.props.targets;
var tooltip = d3.select("body").append("div")
.attr("class", "mpld3-tooltip")
.style("position", "absolute")
.style("z-index", "10")
.style("visibility", "hidden");
obj.elements()
.on("mouseover", function(d, i){
if ($(obj.elements()[0][0]).css( "fill-opacity" ) > 0 || $(obj.elements()[0][0]).css( "stroke-opacity" ) > 0) {
tooltip.html(labels[i])
.style("visibility", "visible");
} })
.on("mousedown", function(d, i){
window.open().document.write(targets[i]);
})
.on("mousemove", function(d, i){
tooltip
.style("top", d3.event.pageY + this.props.voffset + "px")
.style("left",d3.event.pageX + this.props.hoffset + "px");
}.bind(this))
.on("mouseout", function(d, i){
tooltip.style("visibility", "hidden");});
};
mpld3.register_plugin("interactive_legend", InteractiveLegend);
InteractiveLegend.prototype = Object.create(mpld3.Plugin.prototype);
InteractiveLegend.prototype.constructor = InteractiveLegend;
InteractiveLegend.prototype.requiredProps = ["element_ids", "labels"];
InteractiveLegend.prototype.defaultProps = {"ax":null,
"alpha_unsel":0.2,
"alpha_over":1.0,
"start_visible":true}
function InteractiveLegend(fig, props){
mpld3.Plugin.call(this, fig, props);
};
InteractiveLegend.prototype.draw = function(){
var alpha_unsel = this.props.alpha_unsel;
var alpha_over = this.props.alpha_over;
var legendItems = new Array();
for(var i=0; i<this.props.labels.length; i++){
var obj = {};
obj.label = this.props.labels[i];
var element_id = this.props.element_ids[i];
mpld3_elements = [];
for(var j=0; j<element_id.length; j++){
var mpld3_element = mpld3.get_element(element_id[j], this.fig);
// mpld3_element might be null in case of Line2D instances
// for we pass the id for both the line and the markers. Either
// one might not exist on the D3 side
if(mpld3_element){
mpld3_elements.push(mpld3_element);
}
}
obj.mpld3_elements = mpld3_elements;
obj.visible = this.props.start_visible[i]; // should become be setable from python side
legendItems.push(obj);
set_alphas(obj, false);
}
// determine the axes with which this legend is associated
var ax = this.props.ax
if(!ax){
ax = this.fig.axes[0];
} else{
ax = mpld3.get_element(ax, this.fig);
}
// add a legend group to the canvas of the figure
var legend = this.fig.canvas.append("svg:g")
.attr("class", "legend");
// add the rectangles
legend.selectAll("rect")
.data(legendItems)
.enter().append("rect")
.attr("height", 10)
.attr("width", 25)
.attr("x", ax.width + ax.position[0] + 25)
.attr("y",function(d,i) {
return ax.position[1] + i * 25 + 10;})
.attr("stroke", get_color)
.attr("class", "legend-box")
.style("fill", function(d, i) {
return d.visible ? get_color(d) : "white";})
.on("click", click).on('mouseover', over).on('mouseout', out);
// add the labels
legend.selectAll("text")
.data(legendItems)
.enter().append("text")
.attr("x", function (d) {
return ax.width + ax.position[0] + 25 + 40;})
.attr("y", function(d,i) {
return ax.position[1] + i * 25 + 10 + 10 - 1;})
.text(function(d) { return d.label });
// specify the action on click
function click(d,i){
d.visible = !d.visible;
d3.select(this)
.style("fill",function(d, i) {
return d.visible ? get_color(d) : "white";
})
set_alphas(d, false);
};
// specify the action on legend overlay
function over(d,i){
set_alphas(d, true);
};
// specify the action on legend overlay
function out(d,i){
set_alphas(d, false);
};
// helper function for setting alphas
function set_alphas(d, is_over){
for(var i=0; i<d.mpld3_elements.length; i++){
var type = d.mpld3_elements[i].constructor.name;
if(type =="mpld3_Line"){
var current_alpha = d.mpld3_elements[i].props.alpha;
var current_alpha_unsel = current_alpha * alpha_unsel;
var current_alpha_over = current_alpha * alpha_over;
d3.select(d.mpld3_elements[i].path[0][0])
.style("stroke-opacity", is_over ? current_alpha_over :
(d.visible ? current_alpha : current_alpha_unsel))
.style("stroke-width", is_over ?
alpha_over * d.mpld3_elements[i].props.edgewidth : d.mpld3_elements[i].props.edgewidth);
} else if((type=="mpld3_PathCollection")||
(type=="mpld3_Markers")){
var current_alpha = d.mpld3_elements[i].props.alphas[0];
var current_alpha_unsel = current_alpha * alpha_unsel;
var current_alpha_over = current_alpha * alpha_over;
d3.selectAll(d.mpld3_elements[i].pathsobj[0])
.style("stroke-opacity", is_over ? current_alpha_over :
(d.visible ? current_alpha : current_alpha_unsel))
.style("fill-opacity", is_over ? current_alpha_over :
(d.visible ? current_alpha : current_alpha_unsel));
} else{
console.log(type + " not yet supported");
}
}
};
// helper function for determining the color of the rectangles
function get_color(d){
var type = d.mpld3_elements[0].constructor.name;
var color = "black";
if(type =="mpld3_Line"){
color = d.mpld3_elements[0].props.edgecolor;
} else if((type=="mpld3_PathCollection")||
(type=="mpld3_Markers")){
color = d.mpld3_elements[0].props.facecolors[0];
} else{
console.log(type + " not yet supported");
}
return color;
};
};
mpld3.register_plugin("mousexposition", MouseXPositionPlugin);
MouseXPositionPlugin.prototype = Object.create(mpld3.Plugin.prototype);
MouseXPositionPlugin.prototype.constructor = MouseXPositionPlugin;
MouseXPositionPlugin.prototype.requiredProps = [];
MouseXPositionPlugin.prototype.defaultProps = {
fontsize: 12,
fmt: "0d"
};
function MouseXPositionPlugin(fig, props) {
mpld3.Plugin.call(this, fig, props);
}
MouseXPositionPlugin.prototype.draw = function() {
var fig = this.fig;
var fmt = d3.format(this.props.fmt);
var coords = fig.canvas.append("text").attr("class", "mpld3-coordinates").style("text-anchor", "end").style("font-size", this.props.fontsize).attr("x", this.fig.width - 5).attr("y", this.fig.height - 5);
for (var i = 0; i < this.fig.axes.length; i++) {
var update_coords = function() {
var ax = fig.axes[i];
return function() {
var pos = d3.mouse(this), x = ax.x.invert(pos[0]), y = ax.y.invert(pos[1]);
coords.text("AA residue " + fmt(x));
};
}();
fig.axes[i].baseaxes.on("mousemove", update_coords).on("mouseout", function() {
coords.text("");
});
}
};
mpld3.draw_figure("fig_el320884549039056450069957", {"axes": [{"xlim": [0.0, 857.0], "yscale": "linear", "axesbg": "#FFFFFF", "texts": [{"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "ELAVL1", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [325.19999999999999, 23.300000000000001], "rotation": -0.0, "id": "el320884638016400"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF4", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [493.19999999999999, 5.2999999999999998], "rotation": -0.0, "id": "el320884638017360"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF1", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [247.19999999999999, 4.2999999999999998], "rotation": -0.0, "id": "el320884638018064"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPA0", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [304.19999999999999, 6.2999999999999998], "rotation": -0.0, "id": "el320884638018896"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPDL", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [419.19999999999999, 12.300000000000001], "rotation": -0.0, "id": "el320884549168144"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPF", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [414.19999999999999, 18.300000000000001], "rotation": -0.0, "id": "el320884638016336"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPA2B1", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [352.19999999999999, 1.3], "rotation": -0.0, "id": "el320884634227600"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPM", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [729.20000000000005, 17.300000000000001], "rotation": -0.0, "id": "el320884634228816"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPH1", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [448.19999999999999, 16.300000000000001], "rotation": -0.0, "id": "el320884634229904"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPH3", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [345.19999999999999, 2.2999999999999998], "rotation": -0.0, "id": "el320884638253264"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPAB", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [331.19999999999999, 13.300000000000001], "rotation": -0.0, "id": "el320884638254352"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "ELAVL4", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [379.19999999999999, 15.300000000000001], "rotation": -0.0, "id": "el320884638255504"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPH2", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [448.19999999999999, 20.300000000000001], "rotation": -0.0, "id": "el320884638179728"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "ELAVL2", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [358.19999999999999, 21.300000000000001], "rotation": -0.0, "id": "el320884638181008"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF11", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [483.19999999999999, 35.299999999999997], "rotation": -0.0, "id": "el320884624647184"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPK", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [462.19999999999999, 25.300000000000001], "rotation": -0.0, "id": "el320884624648336"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPUL1", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [855.20000000000005, 28.300000000000001], "rotation": -0.0, "id": "el320884624649488"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPA1L2", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [319.19999999999999, 11.300000000000001], "rotation": -0.0, "id": "el320884638575888"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPLL", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [541.20000000000005, 24.300000000000001], "rotation": -0.0, "id": "el320884638573008"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPR", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [632.20000000000005, 19.300000000000001], "rotation": -0.0, "id": "el320884638574096"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF10", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [261.19999999999999, 30.300000000000001], "rotation": -0.0, "id": "el320884638575184"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPA1", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [371.19999999999999, 0.29999999999999999], "rotation": -0.0, "id": "el320884625954256"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPL", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [588.20000000000005, 14.300000000000001], "rotation": -0.0, "id": "el320884625955536"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPCL1", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [292.19999999999999, 32.299999999999997], "rotation": -0.0, "id": "el320884625956816"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF12", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [260.19999999999999, 36.299999999999997], "rotation": -0.0, "id": "el320884626023632"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPC", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [305.19999999999999, 31.300000000000001], "rotation": -0.0, "id": "el320884626025104"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPUL2", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [746.20000000000005, 27.300000000000001], "rotation": -0.0, "id": "el320884626026384"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF2", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [220.19999999999999, 33.299999999999997], "rotation": -0.0, "id": "el320884625798288"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPU", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [824.20000000000005, 26.300000000000001], "rotation": -0.0, "id": "el320884625799504"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPA3", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [377.19999999999999, 3.2999999999999998], "rotation": -0.0, "id": "el320884624606288"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF6", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [343.19999999999999, 9.3000000000000007], "rotation": -0.0, "id": "el320884549667728"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "ELAVL3", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [366.19999999999999, 22.300000000000001], "rotation": -0.0, "id": "el320884549664912"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF5", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [271.19999999999999, 8.3000000000000007], "rotation": -0.0, "id": "el320884624508112"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF9", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [220.19999999999999, 7.2999999999999998], "rotation": -0.0, "id": "el320884634680336"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF3", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [163.19999999999999, 34.299999999999997], "rotation": -0.0, "id": "el320884625639760"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "HNRNPD", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [354.19999999999999, 10.300000000000001], "rotation": -0.0, "id": "el320884637992400"}, {"v_baseline": "auto", "h_anchor": "end", "color": "#262626", "text": "SRSF7", "coordinates": "data", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [237.19999999999999, 29.300000000000001], "rotation": -0.0, "id": "el320884625800400"}, {"v_baseline": "auto", "h_anchor": "middle", "color": "#262626", "text": "Figure 2", "coordinates": "axes", "zorder": 3, "alpha": 1, "fontsize": 12.0, "position": [0.5, 1.0041708375041709], "rotation": -0.0, "id": "el320884580332432"}], "zoomable": true, "images": [], "xdomain": [0.0, 857.0], "ylim": [0.0, 37.0], "paths": [{"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data01", "id": "el320884580103184"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data02", "id": "el320884499404176"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data03", "id": "el320884518182416"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data04", "id": "el320884546998416"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data05", "id": "el320884499639888"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data06", "id": "el320884548764752"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data07", "id": "el320884580915728"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data08", "id": "el320884580163536"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data09", "id": "el320884633060688"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data10", "id": "el320884549917136"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data11", "id": "el320884626477200"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data12", "id": "el320884517927248"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data13", "id": "el320884633500688"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data14", "id": "el320884633144848"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 2, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data11", "id": "el320884580357456"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data15", "id": "el320884634205200"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], "yindex": 1, "coordinates": "data", "dasharray": "none", "zorder": 1, "alpha": 1, "xindex": 0, "data": "data16", "id": "el320884632729424"}, {"edgecolor": "#000000", "facecolor": "#F8F8FF", "edgewidth": 0.3, "pathcodes": ["M", "L", "L", "L", "Z"], 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{"voffset": 10, "labels": ["RRM 3"], "hoffset": 0, "location": "mouse", "type": "tooltip", "id": "el320884626479760"}, {"voffset": 10, "labels": ["RRM 3"], "hoffset": 0, "location": "mouse", "type": "tooltip", "id": "el320884633499984"}, {"voffset": 10, "labels": ["RRM 3"], "hoffset": 0, "location": "mouse", "type": "tooltip", "id": "el320884633498704"}, {"voffset": 10, "labels": ["RRM 3"], "hoffset": 0, "location": "mouse", "type": "tooltip", "id": "el320884549899024"}, {"voffset": 10, "labels": ["RRM 3"], "hoffset": 0, "location": "mouse", "type": "tooltip", "id": "el320884548431632"}, {"voffset": 10, "labels": ["RRM 3"], "hoffset": 0, "location": "mouse", "type": "tooltip", "id": "el320884634677392"}, {"voffset": 10, "labels": ["RRM 3"], "hoffset": 0, "location": "mouse", "type": "tooltip", "id": "el320884625639248"}, {"voffset": 10, "labels": ["RRM 3"], "hoffset": 0, "location": "mouse", "type": "tooltip", "id": "el320884653222096"}, {"voffset": -6, "labels": ["Phosphoserine", 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2</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q15717</h1><br><h2>ELAVL1 HUR</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 202</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q08170</h1><br><h2>SRSF4 SFRS4 SRP75</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 78</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q08170</h1><br><h2>SRSF4 SFRS4 SRP75</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 431</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q08170</h1><br><h2>SRSF4 SFRS4 SRP75</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 446</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q08170</h1><br><h2>SRSF4 SFRS4 SRP75</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 458</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q07955</h1><br><h2>SRSF1 ASF SF2 SF2P33 SFRS1 OK/SW-cl.3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 2</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q07955</h1><br><h2>SRSF1 ASF SF2 SF2P33 SFRS1 OK/SW-cl.3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 199</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q07955</h1><br><h2>SRSF1 ASF SF2 SF2P33 SFRS1 OK/SW-cl.3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 201</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q07955</h1><br><h2>SRSF1 ASF SF2 SF2P33 SFRS1 OK/SW-cl.3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 205</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q07955</h1><br><h2>SRSF1 ASF SF2 SF2P33 SFRS1 OK/SW-cl.3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 231</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q07955</h1><br><h2>SRSF1 ASF SF2 SF2P33 SFRS1 OK/SW-cl.3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 234</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q07955</h1><br><h2>SRSF1 ASF SF2 SF2P33 SFRS1 OK/SW-cl.3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 238</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13151</h1><br><h2>HNRNPA0 HNRPA0</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 68</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13151</h1><br><h2>HNRNPA0 HNRPA0</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 84</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20932473\">PubMed</a></td>\n <td><br />1. Mol Cell. 2010 Oct 8;40(1):34-49. doi: 10.1016/j.molcel.2010.09.018.<br /><br />DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint <br />network controlled by MK2-mediated RNA stabilization.<br /><br />Reinhardt HC(1), Hasskamp P, Schmedding I, Morandell S, van Vugt MA, Wang X,<br />Linding R, Ong SE, Weaver D, Carr SA, Yaffe MB.<br /><br />Author information: <br />(1)David H. Koch Institute for Integrative Cancer Research, Department of<br />Biology, Massachusetts Institute of Technology, Cambridge, MA 02132, USA.<br /><br />Following genotoxic stress, cells activate a complex kinase-based signaling<br />network to arrest the cell cycle and initiate DNA repair. p53-defective tumor<br />cells rewire their checkpoint response and become dependent on the p38/MK2<br />pathway for survival after DNA damage, despite a functional ATR-Chk1 pathway. We <br />used functional genetics to dissect the contributions of Chk1 and MK2 to<br />checkpoint control. We show that nuclear Chk1 activity is essential to establish <br />a G(2)/M checkpoint, while cytoplasmic MK2 activity is critical for prolonged<br />checkpoint maintenance through a process of posttranscriptional mRNA<br />stabilization. Following DNA damage, the p38/MK2 complex relocalizes from nucleus<br />to cytoplasm where MK2 phosphorylates hnRNPA0, to stabilize Gadd45\u03b1 mRNA, while<br />p38 phosphorylates and releases the translational inhibitor TIAR. In addition,<br />MK2 phosphorylates PARN, blocking Gadd45\u03b1 mRNA degradation. Gadd45\u03b1 functions<br />within a positive feedback loop, sustaining the MK2-dependent cytoplasmic<br />sequestration of Cdc25B/C to block mitotic entry in the presence of unrepaired<br />DNA damage. Our findings demonstrate a critical role for the MK2 pathway in the<br />posttranscriptional regulation of gene expression as part of the DNA damage<br />response in cancer cells.<br /><br />Copyright \u00a9 2010 Elsevier Inc. All rights reserved.<br /><br />PMCID: PMC3030122<br />PMID: 20932473 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13151</h1><br><h2>HNRNPA0 HNRPA0</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 188</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>O14979</h1><br><h2>HNRNPDL HNRPDL JKTBP</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 160</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td>UniProtKB:Q99729</td>\n <td></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>O14979</h1><br><h2>HNRNPDL HNRPDL JKTBP</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 241</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52597</h1><br><h2>HNRNPF HNRPF</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 104</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19369195\">PubMed</a></td>\n <td><br />1. Mol Cell Proteomics. 2009 Jul;8(7):1751-64. doi: 10.1074/mcp.M800588-MCP200. Epub<br />2009 Apr 15.<br /><br />Large-scale proteomics analysis of the human kinome.<br /><br />Oppermann FS(1), Gnad F, Olsen JV, Hornberger R, Greff Z, K\u00e9ri G, Mann M, Daub H.<br /><br />Author information: <br />(1)Department of Molecular Biology, Max Planck Institute of Biochemistry,<br />Martinsried, Germany.<br /><br />Members of the human protein kinase superfamily are the major regulatory enzymes <br />involved in the activity control of eukaryotic signal transduction pathways. As<br />protein kinases reside at the nodes of phosphorylation-based signal transmission,<br />comprehensive analysis of their cellular expression and site-specific<br />phosphorylation can provide important insights into the architecture and<br />functionality of signaling networks. However, in global proteome studies, low<br />cellular abundance of protein kinases often results in rather minor peptide<br />species that are occluded by a vast excess of peptides from other cellular<br />proteins. These analytical limitations create a rationale for kinome-wide<br />enrichment of protein kinases prior to mass spectrometry analysis. Here, we<br />employed stable isotope labeling by amino acids in cell culture (SILAC) to<br />compare the binding characteristics of three kinase-selective affinity resins by <br />quantitative mass spectrometry. The evaluated pre-fractionation tools possessed<br />pyrido[2,3-d]pyrimidine-based kinase inhibitors as immobilized capture ligands<br />and retained considerable subsets of the human kinome. Based on these results, an<br />affinity resin displaying the broadly selective kinase ligand VI16832 was<br />employed to quantify the relative expression of more than 170 protein kinases<br />across three different, SILAC-encoded cancer cell lines. These experiments<br />demonstrated the feasibility of comparative kinome profiling in a compact<br />experimental format. Interestingly, we found high levels of cytoplasmic and low<br />levels of receptor tyrosine kinases in MV4-11 leukemia cells compared with the<br />adherent cancer lines HCT116 and MDA-MB-435S. The VI16832 resin was further<br />exploited to pre-fractionate kinases for targeted phosphoproteomics analysis,<br />which revealed about 1200 distinct phosphorylation sites on more than 200 protein<br />kinases. This hitherto largest survey of site-specific phosphorylation across the<br />kinome significantly expands the basis for functional follow-up studies on<br />protein kinase regulation. In conclusion, the straightforward experimental<br />procedures described here enable different implementations of kinase-selective<br />proteomics with considerable potential for future signal transduction and kinase <br />drug target analysis.<br /><br />PMCID: PMC2709199<br />PMID: 19369195 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52597</h1><br><h2>HNRNPF HNRPF</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 161</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17525332\">PubMed</a></td>\n <td><br />1. Science. 2007 May 25;316(5828):1160-6.<br /><br />ATM and ATR substrate analysis reveals extensive protein networks responsive to<br />DNA damage.<br /><br />Matsuoka S(1), Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J,<br />Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ.<br /><br />Author information: <br />(1)Department of Genetics and Center for Genetics and Genomics, Brigham and<br />Women's Hospital, Howard Hughes Medical Institute, Harvard Medical School,<br />Boston, MA 02115, USA.<br /><br />Comment in<br /> Science. 2007 May 25;316(5828):1138-9.<br /><br />Cellular responses to DNA damage are mediated by a number of protein kinases,<br />including ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3-related). The<br />outlines of the signal transduction portion of this pathway are known, but little<br />is known about the physiological scope of the DNA damage response (DDR). We<br />performed a large-scale proteomic analysis of proteins phosphorylated in response<br />to DNA damage on consensus sites recognized by ATM and ATR and identified more<br />than 900 regulated phosphorylation sites encompassing over 700 proteins.<br />Functional analysis of a subset of this data set indicated that this list is<br />highly enriched for proteins involved in the DDR. This set of proteins is highly <br />interconnected, and we identified a large number of protein modules and networks <br />not previously linked to the DDR. This database paints a much broader landscape<br />for the DDR than was previously appreciated and opens new avenues of<br />investigation into the responses to DNA damage in mammals.<br /><br />PMID: 17525332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52597</h1><br><h2>HNRNPF HNRPF</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 187</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 29</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 85</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 149</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 212</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 225</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 231</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 236</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 259</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17924679\">PubMed</a></td>\n <td><br />1. J Proteome Res. 2007 Nov;6(11):4150-62. Epub 2007 Oct 9.<br /><br />Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high <br />confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS<br />spectra.<br /><br />Yu LR(1), Zhu Z, Chan KC, Issaq HJ, Dimitrov DS, Veenstra TD.<br /><br />Author information: <br />(1)Laboratory of Proteomics and Analytical Technologies, Advanced Technology<br />Program, SAIC-Frederick, Inc., NCI-Frederick, P.O. Box B, Frederick, Maryland<br />21702, USA. lyu@ncifcrf.gov<br /><br />Enrichment is essential for phosphoproteome analysis because phosphorylated<br />proteins are usually present in cells in low abundance. Recently, titanium<br />dioxide (TiO2) has been demonstrated to enrich phosphopeptides from simple<br />peptide mixtures with high specificity; however, the technology has not been<br />optimized. In the present study, significant non-specific bindings were observed <br />when proteome samples were applied to TiO2 columns. Column wash with an NH4Glu<br />solution after loading peptide mixtures significantly increased the efficiency of<br />TiO2 phosphopeptide enrichment with a recovery of up to 84%. Also, for proteome<br />samples, more than a 2-fold increase in unique phosphopeptide identifications has<br />been achieved. The use of NH4Glu for a TiO2 column wash does not significantly<br />reduce the phosphopeptide recovery. A total of 858 phosphopeptides corresponding <br />to 1034 distinct phosphosites has been identified from HeLa cells using the<br />improved TiO2 enrichment procedure in combination with data-dependent neutral<br />loss nano-RPLC-MS2-MS3 analysis. While 41 and 35% of the phosphopeptides were<br />identified only by MS2 and MS3, respectively, 24% was identified by both MS2 and <br />MS3. Cross-validation of the phosphopeptide assignment by MS2 and MS3 scans<br />resulted in the highest confidence in identification (99.5%). Many phosphosites<br />identified in this study appear to be novel, including sites from antigen Ki-67, <br />nucleolar phosphoprotein p130, and Treacle protein. The study also indicates that<br />evaluation of confidence levels for phosphopeptide identification via the<br />reversed sequence database searching strategy might underestimate the false<br />positive rate.<br /><br />PMID: 17924679 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18220336\">PubMed</a></td>\n <td><br />1. J Proteome Res. 2008 Mar;7(3):1346-51. doi: 10.1021/pr0705441. Epub 2008 Jan 26.<br /><br />Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient<br />phosphoproteomic analysis.<br /><br />Cantin GT(1), Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd.<br /><br />Author information: <br />(1)Departments of Cell Biology, The Scripps Research Institute, 10550 North<br />Torrey Pines Road, La Jolla, California 92037, USA.<br /><br />Immobilized metal affinity chromatography (IMAC) is a common strategy used for<br />the enrichment of phosphopeptides from digested protein mixtures. However, this<br />strategy by itself is inefficient when analyzing complex protein mixtures. Here, <br />we assess the effectiveness of using protein-based IMAC as a pre-enrichment step <br />prior to peptide-based IMAC. Ultimately, we couple the two IMAC-based enrichments<br />and MudPIT in a quantitative phosphoproteomic analysis of the epidermal growth<br />factor pathway in mammalian cells identifying 4470 unique phosphopeptides<br />containing 4729 phosphorylation sites.<br /><br />PMID: 18220336 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19369195\">PubMed</a></td>\n <td><br />1. Mol Cell Proteomics. 2009 Jul;8(7):1751-64. doi: 10.1074/mcp.M800588-MCP200. Epub<br />2009 Apr 15.<br /><br />Large-scale proteomics analysis of the human kinome.<br /><br />Oppermann FS(1), Gnad F, Olsen JV, Hornberger R, Greff Z, K\u00e9ri G, Mann M, Daub H.<br /><br />Author information: <br />(1)Department of Molecular Biology, Max Planck Institute of Biochemistry,<br />Martinsried, Germany.<br /><br />Members of the human protein kinase superfamily are the major regulatory enzymes <br />involved in the activity control of eukaryotic signal transduction pathways. As<br />protein kinases reside at the nodes of phosphorylation-based signal transmission,<br />comprehensive analysis of their cellular expression and site-specific<br />phosphorylation can provide important insights into the architecture and<br />functionality of signaling networks. However, in global proteome studies, low<br />cellular abundance of protein kinases often results in rather minor peptide<br />species that are occluded by a vast excess of peptides from other cellular<br />proteins. These analytical limitations create a rationale for kinome-wide<br />enrichment of protein kinases prior to mass spectrometry analysis. Here, we<br />employed stable isotope labeling by amino acids in cell culture (SILAC) to<br />compare the binding characteristics of three kinase-selective affinity resins by <br />quantitative mass spectrometry. The evaluated pre-fractionation tools possessed<br />pyrido[2,3-d]pyrimidine-based kinase inhibitors as immobilized capture ligands<br />and retained considerable subsets of the human kinome. Based on these results, an<br />affinity resin displaying the broadly selective kinase ligand VI16832 was<br />employed to quantify the relative expression of more than 170 protein kinases<br />across three different, SILAC-encoded cancer cell lines. These experiments<br />demonstrated the feasibility of comparative kinome profiling in a compact<br />experimental format. Interestingly, we found high levels of cytoplasmic and low<br />levels of receptor tyrosine kinases in MV4-11 leukemia cells compared with the<br />adherent cancer lines HCT116 and MDA-MB-435S. The VI16832 resin was further<br />exploited to pre-fractionate kinases for targeted phosphoproteomics analysis,<br />which revealed about 1200 distinct phosphorylation sites on more than 200 protein<br />kinases. This hitherto largest survey of site-specific phosphorylation across the<br />kinome significantly expands the basis for functional follow-up studies on<br />protein kinase regulation. In conclusion, the straightforward experimental<br />procedures described here enable different implementations of kinase-selective<br />proteomics with considerable potential for future signal transduction and kinase <br />drug target analysis.<br /><br />PMCID: PMC2709199<br />PMID: 19369195 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 324</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 341</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17924679\">PubMed</a></td>\n <td><br />1. J Proteome Res. 2007 Nov;6(11):4150-62. Epub 2007 Oct 9.<br /><br />Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high <br />confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS<br />spectra.<br /><br />Yu LR(1), Zhu Z, Chan KC, Issaq HJ, Dimitrov DS, Veenstra TD.<br /><br />Author information: <br />(1)Laboratory of Proteomics and Analytical Technologies, Advanced Technology<br />Program, SAIC-Frederick, Inc., NCI-Frederick, P.O. Box B, Frederick, Maryland<br />21702, USA. lyu@ncifcrf.gov<br /><br />Enrichment is essential for phosphoproteome analysis because phosphorylated<br />proteins are usually present in cells in low abundance. Recently, titanium<br />dioxide (TiO2) has been demonstrated to enrich phosphopeptides from simple<br />peptide mixtures with high specificity; however, the technology has not been<br />optimized. In the present study, significant non-specific bindings were observed <br />when proteome samples were applied to TiO2 columns. Column wash with an NH4Glu<br />solution after loading peptide mixtures significantly increased the efficiency of<br />TiO2 phosphopeptide enrichment with a recovery of up to 84%. Also, for proteome<br />samples, more than a 2-fold increase in unique phosphopeptide identifications has<br />been achieved. The use of NH4Glu for a TiO2 column wash does not significantly<br />reduce the phosphopeptide recovery. A total of 858 phosphopeptides corresponding <br />to 1034 distinct phosphosites has been identified from HeLa cells using the<br />improved TiO2 enrichment procedure in combination with data-dependent neutral<br />loss nano-RPLC-MS2-MS3 analysis. While 41 and 35% of the phosphopeptides were<br />identified only by MS2 and MS3, respectively, 24% was identified by both MS2 and <br />MS3. Cross-validation of the phosphopeptide assignment by MS2 and MS3 scans<br />resulted in the highest confidence in identification (99.5%). Many phosphosites<br />identified in this study appear to be novel, including sites from antigen Ki-67, <br />nucleolar phosphoprotein p130, and Treacle protein. The study also indicates that<br />evaluation of confidence levels for phosphopeptide identification via the<br />reversed sequence database searching strategy might underestimate the false<br />positive rate.<br /><br />PMID: 17924679 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18220336\">PubMed</a></td>\n <td><br />1. J Proteome Res. 2008 Mar;7(3):1346-51. doi: 10.1021/pr0705441. Epub 2008 Jan 26.<br /><br />Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient<br />phosphoproteomic analysis.<br /><br />Cantin GT(1), Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd.<br /><br />Author information: <br />(1)Departments of Cell Biology, The Scripps Research Institute, 10550 North<br />Torrey Pines Road, La Jolla, California 92037, USA.<br /><br />Immobilized metal affinity chromatography (IMAC) is a common strategy used for<br />the enrichment of phosphopeptides from digested protein mixtures. However, this<br />strategy by itself is inefficient when analyzing complex protein mixtures. Here, <br />we assess the effectiveness of using protein-based IMAC as a pre-enrichment step <br />prior to peptide-based IMAC. Ultimately, we couple the two IMAC-based enrichments<br />and MudPIT in a quantitative phosphoproteomic analysis of the epidermal growth<br />factor pathway in mammalian cells identifying 4470 unique phosphopeptides<br />containing 4729 phosphorylation sites.<br /><br />PMID: 18220336 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P22626</h1><br><h2>HNRNPA2B1 HNRPA2B1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 344</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 29</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 365</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 397</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 432</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 452</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 468</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 481</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 528</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 575</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 588</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 618</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 633</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 637</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P52272</h1><br><h2>HNRNPM HNRPM NAGR1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 701</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P31943</h1><br><h2>HNRNPH1 HNRPH HNRPH1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 23</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P31943</h1><br><h2>HNRNPH1 HNRPH HNRPH1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 63</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P31943</h1><br><h2>HNRNPH1 HNRPH HNRPH1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 104</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td>UniProtKB:P52597</td>\n <td></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P31943</h1><br><h2>HNRNPH1 HNRPH HNRPH1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 161</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td>UniProtKB:P52597</td>\n <td></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P31943</h1><br><h2>HNRNPH1 HNRPH HNRPH1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 187</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td>UniProtKB:P52597</td>\n <td></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P31943</h1><br><h2>HNRNPH1 HNRPH HNRPH1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 310</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td>UniProtKB:P55795</td>\n <td></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P31942</h1><br><h2>HNRNPH3 HNRPH3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 216</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19369195\">PubMed</a></td>\n <td><br />1. Mol Cell Proteomics. 2009 Jul;8(7):1751-64. doi: 10.1074/mcp.M800588-MCP200. Epub<br />2009 Apr 15.<br /><br />Large-scale proteomics analysis of the human kinome.<br /><br />Oppermann FS(1), Gnad F, Olsen JV, Hornberger R, Greff Z, K\u00e9ri G, Mann M, Daub H.<br /><br />Author information: <br />(1)Department of Molecular Biology, Max Planck Institute of Biochemistry,<br />Martinsried, Germany.<br /><br />Members of the human protein kinase superfamily are the major regulatory enzymes <br />involved in the activity control of eukaryotic signal transduction pathways. As<br />protein kinases reside at the nodes of phosphorylation-based signal transmission,<br />comprehensive analysis of their cellular expression and site-specific<br />phosphorylation can provide important insights into the architecture and<br />functionality of signaling networks. However, in global proteome studies, low<br />cellular abundance of protein kinases often results in rather minor peptide<br />species that are occluded by a vast excess of peptides from other cellular<br />proteins. These analytical limitations create a rationale for kinome-wide<br />enrichment of protein kinases prior to mass spectrometry analysis. Here, we<br />employed stable isotope labeling by amino acids in cell culture (SILAC) to<br />compare the binding characteristics of three kinase-selective affinity resins by <br />quantitative mass spectrometry. The evaluated pre-fractionation tools possessed<br />pyrido[2,3-d]pyrimidine-based kinase inhibitors as immobilized capture ligands<br />and retained considerable subsets of the human kinome. Based on these results, an<br />affinity resin displaying the broadly selective kinase ligand VI16832 was<br />employed to quantify the relative expression of more than 170 protein kinases<br />across three different, SILAC-encoded cancer cell lines. These experiments<br />demonstrated the feasibility of comparative kinome profiling in a compact<br />experimental format. Interestingly, we found high levels of cytoplasmic and low<br />levels of receptor tyrosine kinases in MV4-11 leukemia cells compared with the<br />adherent cancer lines HCT116 and MDA-MB-435S. The VI16832 resin was further<br />exploited to pre-fractionate kinases for targeted phosphoproteomics analysis,<br />which revealed about 1200 distinct phosphorylation sites on more than 200 protein<br />kinases. This hitherto largest survey of site-specific phosphorylation across the<br />kinome significantly expands the basis for functional follow-up studies on<br />protein kinase regulation. In conclusion, the straightforward experimental<br />procedures described here enable different implementations of kinase-selective<br />proteomics with considerable potential for future signal transduction and kinase <br />drug target analysis.<br /><br />PMCID: PMC2709199<br />PMID: 19369195 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P31942</h1><br><h2>HNRNPH3 HNRPH3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 298</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q99729</h1><br><h2>HNRNPAB ABBP1 HNRPAB</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 81</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q99729</h1><br><h2>HNRNPAB ABBP1 HNRPAB</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 242</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16964243\">PubMed</a></td>\n <td><br />1. Nat Biotechnol. 2006 Oct;24(10):1285-92. Epub 2006 Sep 10.<br /><br />A probability-based approach for high-throughput protein phosphorylation analysis<br />and site localization.<br /><br />Beausoleil SA(1), Vill\u00e9n J, Gerber SA, Rush J, Gygi SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston,<br />Massachusetts 02115, USA.<br /><br />Comment in<br /> Nat Biotechnol. 2006 Oct;24(10):1226-7.<br /><br />Data analysis and interpretation remain major logistical challenges when<br />attempting to identify large numbers of protein phosphorylation sites by<br />nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS)<br />(Supplementary Figure 1 online). In this report we address challenges that are<br />often only addressable by laborious manual validation, including data set error, <br />data set sensitivity and phosphorylation site localization. We provide a<br />large-scale phosphorylation data set with a measured error rate as determined by <br />the target-decoy approach, we demonstrate an approach to maximize data set<br />sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs),<br />and we present a probability-based score, the Ascore, that measures the<br />probability of correct phosphorylation site localization based on the presence<br />and intensity of site-determining ions in MS/MS spectra. We applied our methods<br />in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we<br />identified 1,761 nonredundant phosphorylation sites from 491 proteins with a<br />peptide false-positive rate of 1.3%.<br /><br />PMID: 16964243 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P55795</h1><br><h2>HNRNPH2 FTP3 HNRPH2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 310</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q12926</h1><br><h2>ELAVL2 HUB</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 221</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q05519</h1><br><h2>SRSF11 SFRS11</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 207</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q05519</h1><br><h2>SRSF11 SFRS11</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 414</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q05519</h1><br><h2>SRSF11 SFRS11</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 434</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q05519</h1><br><h2>SRSF11 SFRS11</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 449</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q05519</h1><br><h2>SRSF11 SFRS11</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 464</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q05519</h1><br><h2>SRSF11 SFRS11</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 483</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P61978</h1><br><h2>HNRNPK HNRPK</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 75</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P61978</h1><br><h2>HNRNPK HNRPK</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 116</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P61978</h1><br><h2>HNRNPK HNRPK</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 214</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P61978</h1><br><h2>HNRNPK HNRPK</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 216</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16964243\">PubMed</a></td>\n <td><br />1. Nat Biotechnol. 2006 Oct;24(10):1285-92. Epub 2006 Sep 10.<br /><br />A probability-based approach for high-throughput protein phosphorylation analysis<br />and site localization.<br /><br />Beausoleil SA(1), Vill\u00e9n J, Gerber SA, Rush J, Gygi SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston,<br />Massachusetts 02115, USA.<br /><br />Comment in<br /> Nat Biotechnol. 2006 Oct;24(10):1226-7.<br /><br />Data analysis and interpretation remain major logistical challenges when<br />attempting to identify large numbers of protein phosphorylation sites by<br />nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS)<br />(Supplementary Figure 1 online). In this report we address challenges that are<br />often only addressable by laborious manual validation, including data set error, <br />data set sensitivity and phosphorylation site localization. We provide a<br />large-scale phosphorylation data set with a measured error rate as determined by <br />the target-decoy approach, we demonstrate an approach to maximize data set<br />sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs),<br />and we present a probability-based score, the Ascore, that measures the<br />probability of correct phosphorylation site localization based on the presence<br />and intensity of site-determining ions in MS/MS spectra. We applied our methods<br />in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we<br />identified 1,761 nonredundant phosphorylation sites from 491 proteins with a<br />peptide false-positive rate of 1.3%.<br /><br />PMID: 16964243 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P61978</h1><br><h2>HNRNPK HNRPK</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 284</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16564677\">PubMed</a></td>\n <td><br />1. Cell Signal. 2006 Oct;18(10):1769-78. Epub 2006 Feb 28.<br /><br />PITK, a PP1 targeting subunit that modulates the phosphorylation of the<br />transcriptional regulator hnRNP K.<br /><br />Kwiek NC(1), Thacker DF, Datto MB, Megosh HB, Haystead TA.<br /><br />Author information: <br />(1)Department of Pharmacology and Cancer Biology, Duke University Medical Center,<br />Box 3813, Durham, NC 27710, USA.<br /><br />Protein phosphatase-1 (PP1), through interactions with substrate targeting<br />subunits, plays critical roles in the regulation of numerous cellular processes. <br />Herein, we describe a newly identified regulatory subunit (PITK; Phosphatase<br />Interactor Targeting K protein) that specifically targets the catalytic subunit<br />of PP1 to nuclear foci to selectively bind and dephosphorylate the<br />transcriptional regulator heterogeneous nuclear ribonucleoprotein K (hnRNP K) at <br />a regulatory S284 site. Additionally, PITK is phosphorylated in vivo at S1013 and<br />S1017, residues that flank or reside within the PP1C-binding motif, and this<br />phosphorylation negatively regulates the binding of the phosphatase to PITK. A<br />mutant variant, S1013,1017A-PITK, when expressed in intact cells, exhibited an<br />increase in native PP1 binding and elicited a more profound dephosphorylation of <br />hnRNPK at S284. A global analysis of transcription by Affymetrix microarray<br />revealed that the expression of PITK resulted in the altered expression of 47<br />genes, including a marked induction of MEK5 (>14-fold, p<0.007). Additionally,<br />the effects of PITK and S1013,1017A-PITK on transcription could be modulated by<br />the co-expression of hnRNP K. Taken together, our findings provide a putative<br />mechanism by which transcriptional activity of hnRNP K can be discretely<br />controlled through the regulation of PP1 activity.<br /><br />PMID: 16564677 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P61978</h1><br><h2>HNRNPK HNRPK</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 379</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16964243\">PubMed</a></td>\n <td><br />1. Nat Biotechnol. 2006 Oct;24(10):1285-92. Epub 2006 Sep 10.<br /><br />A probability-based approach for high-throughput protein phosphorylation analysis<br />and site localization.<br /><br />Beausoleil SA(1), Vill\u00e9n J, Gerber SA, Rush J, Gygi SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston,<br />Massachusetts 02115, USA.<br /><br />Comment in<br /> Nat Biotechnol. 2006 Oct;24(10):1226-7.<br /><br />Data analysis and interpretation remain major logistical challenges when<br />attempting to identify large numbers of protein phosphorylation sites by<br />nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS)<br />(Supplementary Figure 1 online). In this report we address challenges that are<br />often only addressable by laborious manual validation, including data set error, <br />data set sensitivity and phosphorylation site localization. We provide a<br />large-scale phosphorylation data set with a measured error rate as determined by <br />the target-decoy approach, we demonstrate an approach to maximize data set<br />sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs),<br />and we present a probability-based score, the Ascore, that measures the<br />probability of correct phosphorylation site localization based on the presence<br />and intensity of site-determining ions in MS/MS spectra. We applied our methods<br />in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we<br />identified 1,761 nonredundant phosphorylation sites from 491 proteins with a<br />peptide false-positive rate of 1.3%.<br /><br />PMID: 16964243 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q9BUJ2</h1><br><h2>HNRNPUL1 E1BAP5 HNRPUL1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 194</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17693683\">PubMed</a></td>\n <td><br />1. Mol Cell Proteomics. 2007 Nov;6(11):1952-67. Epub 2007 Aug 12.<br /><br />Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network:<br />indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit<br />phosphorylation at residue serine 20 in canonical Wnt signal transduction.<br /><br />Tang LY(1), Deng N, Wang LS, Dai J, Wang ZL, Jiang XS, Li SJ, Li L, Sheng QH, Wu <br />DQ, Li L, Zeng R.<br /><br />Author information: <br />(1)State Key Laboratory of Molecular Biology, Shangai 200031, China.<br /><br />The complexity of canonical Wnt signaling comes not only from the numerous<br />components but also from multiple post-translational modifications. Protein<br />phosphorylation is one of the most common modifications that propagates signals<br />from extracellular stimuli to downstream effectors. To investigate the global<br />phosphorylation regulation and uncover novel phosphoproteins at the early stages <br />of canonical Wnt signaling, HEK293 cells were metabolically labeled with two<br />stable isotopic forms of lysine and were stimulated for 0, 1, or 30 min with<br />purified Wnt3a. After phosphoprotein enrichment and LC-MS/MS analysis, 1057<br />proteins were identified in all three time points. In total 287 proteins showed a<br />1.5-fold or greater change in at least one time point. In addition to many known <br />Wnt signaling transducers, other phosphoproteins were identified and quantitated,<br />implicating their involvement in canonical Wnt signaling. k-Means clustering<br />analysis showed dynamic patterns for the differential phosphoproteins. Profile<br />pattern and interaction network analysis of the differential phosphoproteins<br />implicated the possible roles for those unreported components in Wnt signaling.<br />Moreover 100 unique phosphorylation sites were identified, and 54 of them were<br />quantitated in the three time points. Site-specific phosphopeptide quantitation<br />revealed that Ser-20 phosphorylation on RRM2 increased upon 30-min Wnt3a<br />stimulation. Further studies with mutagenesis, the Wnt reporter gene assay, and<br />RNA interference indicated that RRM2 functioned downstream of beta-catenin as an <br />inhibitor of Wnt signaling and that Ser-20 phosphorylation of RRM2 counteracted<br />its inhibition effect. Our systematic profiling of dynamic phosphorylation<br />changes responding to Wnt3a stimulation not only presented a comprehensive<br />phosphorylation network regulated by canonical Wnt signaling but also found novel<br />molecules and phosphorylation involved in Wnt signaling.<br /><br />PMID: 17693683 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18220336\">PubMed</a></td>\n <td><br />1. J Proteome Res. 2008 Mar;7(3):1346-51. doi: 10.1021/pr0705441. Epub 2008 Jan 26.<br /><br />Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient<br />phosphoproteomic analysis.<br /><br />Cantin GT(1), Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd.<br /><br />Author information: <br />(1)Departments of Cell Biology, The Scripps Research Institute, 10550 North<br />Torrey Pines Road, La Jolla, California 92037, USA.<br /><br />Immobilized metal affinity chromatography (IMAC) is a common strategy used for<br />the enrichment of phosphopeptides from digested protein mixtures. However, this<br />strategy by itself is inefficient when analyzing complex protein mixtures. Here, <br />we assess the effectiveness of using protein-based IMAC as a pre-enrichment step <br />prior to peptide-based IMAC. Ultimately, we couple the two IMAC-based enrichments<br />and MudPIT in a quantitative phosphoproteomic analysis of the epidermal growth<br />factor pathway in mammalian cells identifying 4470 unique phosphopeptides<br />containing 4729 phosphorylation sites.<br /><br />PMID: 18220336 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q9BUJ2</h1><br><h2>HNRNPUL1 E1BAP5 HNRPUL1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 512</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q9BUJ2</h1><br><h2>HNRNPUL1 E1BAP5 HNRPUL1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 718</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q32P51</h1><br><h2>HNRNPA1L2 HNRNPA1L</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 6</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td>UniProtKB:P49312</td>\n <td></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q8WVV9</h1><br><h2>HNRNPLL HNRPLL SRRF BLOCK24</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 68</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>O75494</h1><br><h2>SRSF10 FUSIP1 FUSIP2 SFRS13A TASR</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 106</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>O75494</h1><br><h2>SRSF10 FUSIP1 FUSIP2 SFRS13A TASR</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 108</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>O75494</h1><br><h2>SRSF10 FUSIP1 FUSIP2 SFRS13A TASR</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 129</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>O75494</h1><br><h2>SRSF10 FUSIP1 FUSIP2 SFRS13A TASR</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 131</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>O75494</h1><br><h2>SRSF10 FUSIP1 FUSIP2 SFRS13A TASR</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 133</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19369195\">PubMed</a></td>\n <td><br />1. Mol Cell Proteomics. 2009 Jul;8(7):1751-64. doi: 10.1074/mcp.M800588-MCP200. Epub<br />2009 Apr 15.<br /><br />Large-scale proteomics analysis of the human kinome.<br /><br />Oppermann FS(1), Gnad F, Olsen JV, Hornberger R, Greff Z, K\u00e9ri G, Mann M, Daub H.<br /><br />Author information: <br />(1)Department of Molecular Biology, Max Planck Institute of Biochemistry,<br />Martinsried, Germany.<br /><br />Members of the human protein kinase superfamily are the major regulatory enzymes <br />involved in the activity control of eukaryotic signal transduction pathways. As<br />protein kinases reside at the nodes of phosphorylation-based signal transmission,<br />comprehensive analysis of their cellular expression and site-specific<br />phosphorylation can provide important insights into the architecture and<br />functionality of signaling networks. However, in global proteome studies, low<br />cellular abundance of protein kinases often results in rather minor peptide<br />species that are occluded by a vast excess of peptides from other cellular<br />proteins. These analytical limitations create a rationale for kinome-wide<br />enrichment of protein kinases prior to mass spectrometry analysis. Here, we<br />employed stable isotope labeling by amino acids in cell culture (SILAC) to<br />compare the binding characteristics of three kinase-selective affinity resins by <br />quantitative mass spectrometry. The evaluated pre-fractionation tools possessed<br />pyrido[2,3-d]pyrimidine-based kinase inhibitors as immobilized capture ligands<br />and retained considerable subsets of the human kinome. Based on these results, an<br />affinity resin displaying the broadly selective kinase ligand VI16832 was<br />employed to quantify the relative expression of more than 170 protein kinases<br />across three different, SILAC-encoded cancer cell lines. These experiments<br />demonstrated the feasibility of comparative kinome profiling in a compact<br />experimental format. Interestingly, we found high levels of cytoplasmic and low<br />levels of receptor tyrosine kinases in MV4-11 leukemia cells compared with the<br />adherent cancer lines HCT116 and MDA-MB-435S. The VI16832 resin was further<br />exploited to pre-fractionate kinases for targeted phosphoproteomics analysis,<br />which revealed about 1200 distinct phosphorylation sites on more than 200 protein<br />kinases. This hitherto largest survey of site-specific phosphorylation across the<br />kinome significantly expands the basis for functional follow-up studies on<br />protein kinase regulation. In conclusion, the straightforward experimental<br />procedures described here enable different implementations of kinase-selective<br />proteomics with considerable potential for future signal transduction and kinase <br />drug target analysis.<br /><br />PMCID: PMC2709199<br />PMID: 19369195 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>O75494</h1><br><h2>SRSF10 FUSIP1 FUSIP2 SFRS13A TASR</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 158</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>O75494</h1><br><h2>SRSF10 FUSIP1 FUSIP2 SFRS13A TASR</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 160</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 2</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 4</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 6</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 192</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16111636\">PubMed</a></td>\n <td><br />1. Immunity. 2005 Aug;23(2):177-89.<br /><br />The Mnks are novel components in the control of TNF alpha biosynthesis and<br />phosphorylate and regulate hnRNP A1.<br /><br />Buxad\u00e9 M(1), Parra JL, Rousseau S, Shpiro N, Marquez R, Morrice N, Bain J, Espel <br />E, Proud CG.<br /><br />Author information: <br />(1)Departament de Fisiologia, Universitat de Barcelona, Spain.<br /><br />Posttranscriptional regulatory mechanisms control TNFalpha expression through<br />AU-rich elements in the 3'UTR of its mRNA. This is mediated through Erk and p38<br />MAP kinase signaling, although the mechanisms involved remain poorly understood. <br />Here, we show that the MAP kinase signal-integrating kinases (Mnks), which are<br />activated by both these pathways, regulate TNFalpha expression in T cells via the<br />3'UTR. A selective Mnk inhibitor or siRNA-mediated knockdown of Mnk1 inhibits<br />TNFalpha production in T cells, whereas Mnk1 overexpression enhances expression<br />of a reporter construct containing the TNFalpha 3'UTR. We identify ARE binding<br />proteins that are Mnk substrates, such as hnRNP A1, which they phosphorylate at<br />two sites in vitro. hnRNP A1 is phosphorylated in response to T cell activation, <br />and this is blocked by Mnk inhibition. Moreover, Mnk-mediated phosphorylation<br />decreases binding of hnRNP A1 to TNFalpha-ARE in vitro or TNFalpha-mRNA in vivo. <br />Therefore, Mnks are novel players in cytokine regulation and potential new<br />targets for anti-inflammatory therapy.<br /><br />PMID: 16111636 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 199</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 362</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16111636\">PubMed</a></td>\n <td><br />1. Immunity. 2005 Aug;23(2):177-89.<br /><br />The Mnks are novel components in the control of TNF alpha biosynthesis and<br />phosphorylate and regulate hnRNP A1.<br /><br />Buxad\u00e9 M(1), Parra JL, Rousseau S, Shpiro N, Marquez R, Morrice N, Bain J, Espel <br />E, Proud CG.<br /><br />Author information: <br />(1)Departament de Fisiologia, Universitat de Barcelona, Spain.<br /><br />Posttranscriptional regulatory mechanisms control TNFalpha expression through<br />AU-rich elements in the 3'UTR of its mRNA. This is mediated through Erk and p38<br />MAP kinase signaling, although the mechanisms involved remain poorly understood. <br />Here, we show that the MAP kinase signal-integrating kinases (Mnks), which are<br />activated by both these pathways, regulate TNFalpha expression in T cells via the<br />3'UTR. A selective Mnk inhibitor or siRNA-mediated knockdown of Mnk1 inhibits<br />TNFalpha production in T cells, whereas Mnk1 overexpression enhances expression<br />of a reporter construct containing the TNFalpha 3'UTR. We identify ARE binding<br />proteins that are Mnk substrates, such as hnRNP A1, which they phosphorylate at<br />two sites in vitro. hnRNP A1 is phosphorylated in response to T cell activation, <br />and this is blocked by Mnk inhibition. Moreover, Mnk-mediated phosphorylation<br />decreases binding of hnRNP A1 to TNFalpha-ARE in vitro or TNFalpha-mRNA in vivo. <br />Therefore, Mnks are novel players in cytokine regulation and potential new<br />targets for anti-inflammatory therapy.<br /><br />PMID: 16111636 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 363</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16111636\">PubMed</a></td>\n <td><br />1. Immunity. 2005 Aug;23(2):177-89.<br /><br />The Mnks are novel components in the control of TNF alpha biosynthesis and<br />phosphorylate and regulate hnRNP A1.<br /><br />Buxad\u00e9 M(1), Parra JL, Rousseau S, Shpiro N, Marquez R, Morrice N, Bain J, Espel <br />E, Proud CG.<br /><br />Author information: <br />(1)Departament de Fisiologia, Universitat de Barcelona, Spain.<br /><br />Posttranscriptional regulatory mechanisms control TNFalpha expression through<br />AU-rich elements in the 3'UTR of its mRNA. This is mediated through Erk and p38<br />MAP kinase signaling, although the mechanisms involved remain poorly understood. <br />Here, we show that the MAP kinase signal-integrating kinases (Mnks), which are<br />activated by both these pathways, regulate TNFalpha expression in T cells via the<br />3'UTR. A selective Mnk inhibitor or siRNA-mediated knockdown of Mnk1 inhibits<br />TNFalpha production in T cells, whereas Mnk1 overexpression enhances expression<br />of a reporter construct containing the TNFalpha 3'UTR. We identify ARE binding<br />proteins that are Mnk substrates, such as hnRNP A1, which they phosphorylate at<br />two sites in vitro. hnRNP A1 is phosphorylated in response to T cell activation, <br />and this is blocked by Mnk inhibition. Moreover, Mnk-mediated phosphorylation<br />decreases binding of hnRNP A1 to TNFalpha-ARE in vitro or TNFalpha-mRNA in vivo. <br />Therefore, Mnks are novel players in cytokine regulation and potential new<br />targets for anti-inflammatory therapy.<br /><br />PMID: 16111636 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 364</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16111636\">PubMed</a></td>\n <td><br />1. Immunity. 2005 Aug;23(2):177-89.<br /><br />The Mnks are novel components in the control of TNF alpha biosynthesis and<br />phosphorylate and regulate hnRNP A1.<br /><br />Buxad\u00e9 M(1), Parra JL, Rousseau S, Shpiro N, Marquez R, Morrice N, Bain J, Espel <br />E, Proud CG.<br /><br />Author information: <br />(1)Departament de Fisiologia, Universitat de Barcelona, Spain.<br /><br />Posttranscriptional regulatory mechanisms control TNFalpha expression through<br />AU-rich elements in the 3'UTR of its mRNA. This is mediated through Erk and p38<br />MAP kinase signaling, although the mechanisms involved remain poorly understood. <br />Here, we show that the MAP kinase signal-integrating kinases (Mnks), which are<br />activated by both these pathways, regulate TNFalpha expression in T cells via the<br />3'UTR. A selective Mnk inhibitor or siRNA-mediated knockdown of Mnk1 inhibits<br />TNFalpha production in T cells, whereas Mnk1 overexpression enhances expression<br />of a reporter construct containing the TNFalpha 3'UTR. We identify ARE binding<br />proteins that are Mnk substrates, such as hnRNP A1, which they phosphorylate at<br />two sites in vitro. hnRNP A1 is phosphorylated in response to T cell activation, <br />and this is blocked by Mnk inhibition. Moreover, Mnk-mediated phosphorylation<br />decreases binding of hnRNP A1 to TNFalpha-ARE in vitro or TNFalpha-mRNA in vivo. <br />Therefore, Mnks are novel players in cytokine regulation and potential new<br />targets for anti-inflammatory therapy.<br /><br />PMID: 16111636 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 365</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P09651</h1><br><h2>HNRNPA1 HNRPA1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 368</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P14866</h1><br><h2>HNRNPL HNRPL P/OKcl.14</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 52</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P14866</h1><br><h2>HNRNPL HNRPL P/OKcl.14</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 101</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P14866</h1><br><h2>HNRNPL HNRPL P/OKcl.14</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 185</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P14866</h1><br><h2>HNRNPL HNRPL P/OKcl.14</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 291</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P14866</h1><br><h2>HNRNPL HNRPL P/OKcl.14</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 298</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P14866</h1><br><h2>HNRNPL HNRPL P/OKcl.14</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 544</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/22570490\">PubMed</a></td>\n <td><br />1. J Biol Chem. 2012 Jun 29;287(27):22709-16. doi: 10.1074/jbc.M112.357343. Epub<br />2012 May 8.<br /><br />A conserved serine of heterogeneous nuclear ribonucleoprotein L (hnRNP L)<br />mediates depolarization-regulated alternative splicing of potassium channels.<br /><br />Liu G(1), Razanau A, Hai Y, Yu J, Sohail M, Lobo VG, Chu J, Kung SK, Xie J.<br /><br />Author information: <br />(1)Department of Physiology, Faculty of Medicine, University of Manitoba, 745<br />Bannatyne Ave., Winnipeg, MB R3E 0J9, Canada.<br /><br />Molecular mechanisms of gene regulation underlying the activity-dependent long<br />term changes of cellular electrical properties, such as those during memory, are <br />largely unknown. We have shown that alternative splicing can be dynamically<br />regulated in response to membrane depolarization and Ca(2+)/calmodulin-dependent <br />protein kinase IV (CaMKIV) activation, through special CaM kinase responsive RNA <br />elements. However, proteins that mediate this regulation and how they are<br />affected by CaMKIV are not known. Here we show that the regulation of the stress <br />axis-regulated exon of the Slo1 potassium channel transcripts by membrane<br />depolarization requires a highly conserved CaMKIV target serine (Ser-513) of the <br />heterogeneous ribonucleoprotein L. Ser-513 phosphorylation within the RNA<br />recognition motif 4 enhanced heterogeneous ribonucleoprotein L interaction with<br />the CaMKIV-responsive RNA element 1 of stress axis-regulated exon and inhibited<br />binding of the large subunit of the U2 auxiliary factor U2AF65. Both of these<br />activities were abolished by a S513A mutation. Thus, through Ser-513, membrane<br />depolarization/calcium signaling controls a critical spliceosomal assembly step<br />to regulate the variant subunit composition of potassium channels.<br /><br />PMCID: PMC3391085<br />PMID: 22570490 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 113</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 115</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 162</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 166</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 233</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18318008\">PubMed</a></td>\n <td><br />1. Proteomics. 2008 Apr;8(7):1346-61. doi: 10.1002/pmic.200700884.<br /><br />Large-scale phosphoproteome analysis of human liver tissue by enrichment and<br />fractionation of phosphopeptides with strong anion exchange chromatography.<br /><br />Han G(1), Ye M, Zhou H, Jiang X, Feng S, Jiang X, Tian R, Wan D, Zou H, Gu J.<br /><br />Author information: <br />(1)National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The<br />Chinese Academy of Sciences, Dalian, China.<br /><br />The mixture of phosphopeptides enriched from proteome samples are very complex.<br />To reduce the complexity it is necessary to fractionate the phosphopeptides.<br />However, conventional enrichment methods typically only enrich phosphopeptides<br />but not fractionate phosphopeptides. In this study, the application of strong<br />anion exchange (SAX) chromatography for enrichment and fractionation of<br />phosphopeptides was presented. It was found that phosphopeptides were highly<br />enriched by SAX and majority of unmodified peptides did not bind onto SAX.<br />Compared with Fe(3+) immobilized metal affinity chromatography (Fe(3+)-IMAC),<br />almost double phosphopeptides were identified from the same sample when only one <br />fraction was generated by SAX. SAX and Fe(3+)-IMAC showed the complementarity in <br />enrichment and identification of phosphopeptides. It was also demonstrated that<br />SAX have the ability to fractionate phosphopeptides under gradient elution based <br />on their different interaction with SAX adsorbent. SAX was further applied to<br />enrich and fractionate phosphopeptides in tryptic digest of proteins extracted<br />from human liver tissue adjacent to tumorous region for phosphoproteome<br />profiling. This resulted in the highly confident identification of 274<br />phosphorylation sites from 305 unique phosphopeptides corresponding to 168<br />proteins at false discovery rate (FDR) of 0.96%.<br /><br />PMID: 18318008 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 238</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 239</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 241</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 253</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/12564933\">PubMed</a></td>\n <td><br />1. Biochemistry. 2003 Feb 11;42(5):1301-8.<br /><br />Basal and hydrogen peroxide stimulated sites of phosphorylation in heterogeneous <br />nuclear ribonucleoprotein C1/C2.<br /><br />Stone JR(1), Maki JL, Collins T.<br /><br />Author information: <br />(1)Department of Pathology, Children's Hospital and Brigham & Women's Hospital,<br />Harvard Medical School, Boston, Massachusetts 02115,USA. jrstone@partners.org<br /><br />Hydrogen peroxide (H2O2) is a recently recognized second messenger, which<br />regulates mammalian cell proliferation and migration. The biochemical mechanisms <br />by which mammalian cells sense and respond to low concentrations of H2O2 are<br />poorly understood. Recently, heterogeneous nuclear ribonucleoprotein C1/C2<br />(hnRNP-C1/C2) was found to be rapidly phosphorylated in response to the<br />application of low concentrations of H2O2 to human endothelial cells. Here, using<br />tandem mass spectrometry, four sites of phosphorylation are identified in<br />hnRNP-C1/C2, all of which are in the acidic C-terminal domain of the protein.<br />Under resting conditions, the protein is phosphorylated at S247 and S286. In<br />response to low concentrations of H2O2, there is increased phosphorylation at<br />S240 and at one of the four contiguous serine residues from S225-S228. Studies<br />using a recombinant acidic C-terminal domain of hnRNP-C overexpressed in<br />Escherichia coli demonstrate that protein kinase CK2 phosphorylates hnRNP-C1/C2<br />at S247, while protein kinase A and several protein kinase C isoforms fail to<br />phosphorylate the isolated domain. These findings demonstrate that the acidic<br />C-terminal domain of hnRNP-C1/C2 serves as the site for both basal and stimulated<br />phosphorylation, indicating that this domain may play an important role in the<br />regulation of mRNA binding by hnRNP-C1/C2.<br /><br />PMID: 12564933 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18318008\">PubMed</a></td>\n <td><br />1. Proteomics. 2008 Apr;8(7):1346-61. doi: 10.1002/pmic.200700884.<br /><br />Large-scale phosphoproteome analysis of human liver tissue by enrichment and<br />fractionation of phosphopeptides with strong anion exchange chromatography.<br /><br />Han G(1), Ye M, Zhou H, Jiang X, Feng S, Jiang X, Tian R, Wan D, Zou H, Gu J.<br /><br />Author information: <br />(1)National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The<br />Chinese Academy of Sciences, Dalian, China.<br /><br />The mixture of phosphopeptides enriched from proteome samples are very complex.<br />To reduce the complexity it is necessary to fractionate the phosphopeptides.<br />However, conventional enrichment methods typically only enrich phosphopeptides<br />but not fractionate phosphopeptides. In this study, the application of strong<br />anion exchange (SAX) chromatography for enrichment and fractionation of<br />phosphopeptides was presented. It was found that phosphopeptides were highly<br />enriched by SAX and majority of unmodified peptides did not bind onto SAX.<br />Compared with Fe(3+) immobilized metal affinity chromatography (Fe(3+)-IMAC),<br />almost double phosphopeptides were identified from the same sample when only one <br />fraction was generated by SAX. SAX and Fe(3+)-IMAC showed the complementarity in <br />enrichment and identification of phosphopeptides. It was also demonstrated that<br />SAX have the ability to fractionate phosphopeptides under gradient elution based <br />on their different interaction with SAX adsorbent. SAX was further applied to<br />enrich and fractionate phosphopeptides in tryptic digest of proteins extracted<br />from human liver tissue adjacent to tumorous region for phosphoproteome<br />profiling. This resulted in the highly confident identification of 274<br />phosphorylation sites from 305 unique phosphopeptides corresponding to 168<br />proteins at false discovery rate (FDR) of 0.96%.<br /><br />PMID: 18318008 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 260</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/12564933\">PubMed</a></td>\n <td><br />1. Biochemistry. 2003 Feb 11;42(5):1301-8.<br /><br />Basal and hydrogen peroxide stimulated sites of phosphorylation in heterogeneous <br />nuclear ribonucleoprotein C1/C2.<br /><br />Stone JR(1), Maki JL, Collins T.<br /><br />Author information: <br />(1)Department of Pathology, Children's Hospital and Brigham & Women's Hospital,<br />Harvard Medical School, Boston, Massachusetts 02115,USA. jrstone@partners.org<br /><br />Hydrogen peroxide (H2O2) is a recently recognized second messenger, which<br />regulates mammalian cell proliferation and migration. The biochemical mechanisms <br />by which mammalian cells sense and respond to low concentrations of H2O2 are<br />poorly understood. Recently, heterogeneous nuclear ribonucleoprotein C1/C2<br />(hnRNP-C1/C2) was found to be rapidly phosphorylated in response to the<br />application of low concentrations of H2O2 to human endothelial cells. Here, using<br />tandem mass spectrometry, four sites of phosphorylation are identified in<br />hnRNP-C1/C2, all of which are in the acidic C-terminal domain of the protein.<br />Under resting conditions, the protein is phosphorylated at S247 and S286. In<br />response to low concentrations of H2O2, there is increased phosphorylation at<br />S240 and at one of the four contiguous serine residues from S225-S228. Studies<br />using a recombinant acidic C-terminal domain of hnRNP-C overexpressed in<br />Escherichia coli demonstrate that protein kinase CK2 phosphorylates hnRNP-C1/C2<br />at S247, while protein kinase A and several protein kinase C isoforms fail to<br />phosphorylate the isolated domain. These findings demonstrate that the acidic<br />C-terminal domain of hnRNP-C1/C2 serves as the site for both basal and stimulated<br />phosphorylation, indicating that this domain may play an important role in the<br />regulation of mRNA binding by hnRNP-C1/C2.<br /><br />PMID: 12564933 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17693683\">PubMed</a></td>\n <td><br />1. Mol Cell Proteomics. 2007 Nov;6(11):1952-67. Epub 2007 Aug 12.<br /><br />Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network:<br />indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit<br />phosphorylation at residue serine 20 in canonical Wnt signal transduction.<br /><br />Tang LY(1), Deng N, Wang LS, Dai J, Wang ZL, Jiang XS, Li SJ, Li L, Sheng QH, Wu <br />DQ, Li L, Zeng R.<br /><br />Author information: <br />(1)State Key Laboratory of Molecular Biology, Shangai 200031, China.<br /><br />The complexity of canonical Wnt signaling comes not only from the numerous<br />components but also from multiple post-translational modifications. Protein<br />phosphorylation is one of the most common modifications that propagates signals<br />from extracellular stimuli to downstream effectors. To investigate the global<br />phosphorylation regulation and uncover novel phosphoproteins at the early stages <br />of canonical Wnt signaling, HEK293 cells were metabolically labeled with two<br />stable isotopic forms of lysine and were stimulated for 0, 1, or 30 min with<br />purified Wnt3a. After phosphoprotein enrichment and LC-MS/MS analysis, 1057<br />proteins were identified in all three time points. In total 287 proteins showed a<br />1.5-fold or greater change in at least one time point. In addition to many known <br />Wnt signaling transducers, other phosphoproteins were identified and quantitated,<br />implicating their involvement in canonical Wnt signaling. k-Means clustering<br />analysis showed dynamic patterns for the differential phosphoproteins. Profile<br />pattern and interaction network analysis of the differential phosphoproteins<br />implicated the possible roles for those unreported components in Wnt signaling.<br />Moreover 100 unique phosphorylation sites were identified, and 54 of them were<br />quantitated in the three time points. Site-specific phosphopeptide quantitation<br />revealed that Ser-20 phosphorylation on RRM2 increased upon 30-min Wnt3a<br />stimulation. Further studies with mutagenesis, the Wnt reporter gene assay, and<br />RNA interference indicated that RRM2 functioned downstream of beta-catenin as an <br />inhibitor of Wnt signaling and that Ser-20 phosphorylation of RRM2 counteracted<br />its inhibition effect. Our systematic profiling of dynamic phosphorylation<br />changes responding to Wnt3a stimulation not only presented a comprehensive<br />phosphorylation network regulated by canonical Wnt signaling but also found novel<br />molecules and phosphorylation involved in Wnt signaling.<br /><br />PMID: 17693683 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18318008\">PubMed</a></td>\n <td><br />1. Proteomics. 2008 Apr;8(7):1346-61. doi: 10.1002/pmic.200700884.<br /><br />Large-scale phosphoproteome analysis of human liver tissue by enrichment and<br />fractionation of phosphopeptides with strong anion exchange chromatography.<br /><br />Han G(1), Ye M, Zhou H, Jiang X, Feng S, Jiang X, Tian R, Wan D, Zou H, Gu J.<br /><br />Author information: <br />(1)National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The<br />Chinese Academy of Sciences, Dalian, China.<br /><br />The mixture of phosphopeptides enriched from proteome samples are very complex.<br />To reduce the complexity it is necessary to fractionate the phosphopeptides.<br />However, conventional enrichment methods typically only enrich phosphopeptides<br />but not fractionate phosphopeptides. In this study, the application of strong<br />anion exchange (SAX) chromatography for enrichment and fractionation of<br />phosphopeptides was presented. It was found that phosphopeptides were highly<br />enriched by SAX and majority of unmodified peptides did not bind onto SAX.<br />Compared with Fe(3+) immobilized metal affinity chromatography (Fe(3+)-IMAC),<br />almost double phosphopeptides were identified from the same sample when only one <br />fraction was generated by SAX. SAX and Fe(3+)-IMAC showed the complementarity in <br />enrichment and identification of phosphopeptides. It was also demonstrated that<br />SAX have the ability to fractionate phosphopeptides under gradient elution based <br />on their different interaction with SAX adsorbent. SAX was further applied to<br />enrich and fractionate phosphopeptides in tryptic digest of proteins extracted<br />from human liver tissue adjacent to tumorous region for phosphoproteome<br />profiling. This resulted in the highly confident identification of 274<br />phosphorylation sites from 305 unique phosphopeptides corresponding to 168<br />proteins at false discovery rate (FDR) of 0.96%.<br /><br />PMID: 18318008 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18691976\">PubMed</a></td>\n <td><br />1. Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.<br /><br />Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome <br />across the cell cycle.<br /><br />Daub H(1), Olsen JV, Bairlein M, Gnad F, Oppermann FS, K\u00f6rner R, Greff Z, K\u00e9ri G,<br />Stemmann O, Mann M.<br /><br />Author information: <br />(1)Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of<br />Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. daub@biochem.mpg.de<br /><br />Protein kinases are pivotal regulators of cell signaling that modulate each<br />other's functions and activities through site-specific phosphorylation events.<br />These key regulatory modifications have not been studied comprehensively, because<br />low cellular abundance of kinases has resulted in their underrepresentation in<br />previous phosphoproteome studies. Here, we combine kinase-selective affinity<br />purification with quantitative mass spectrometry to analyze the cell-cycle<br />regulation of protein kinases. This proteomics approach enabled us to quantify<br />219 protein kinases from S and M phase-arrested human cancer cells. We identified<br />more than 1000 phosphorylation sites on protein kinases. Intriguingly, half of<br />all kinase phosphopeptides were upregulated in mitosis. Our data reveal numerous <br />unknown M phase-induced phosphorylation sites on kinases with established mitotic<br />functions. We also find potential phosphorylation networks involving many protein<br />kinases not previously implicated in mitotic progression. These results provide a<br />vastly extended knowledge base for functional studies on kinases and their<br />regulation through site-specific phosphorylation.<br /><br />PMID: 18691976 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 299</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/12564933\">PubMed</a></td>\n <td><br />1. Biochemistry. 2003 Feb 11;42(5):1301-8.<br /><br />Basal and hydrogen peroxide stimulated sites of phosphorylation in heterogeneous <br />nuclear ribonucleoprotein C1/C2.<br /><br />Stone JR(1), Maki JL, Collins T.<br /><br />Author information: <br />(1)Department of Pathology, Children's Hospital and Brigham & Women's Hospital,<br />Harvard Medical School, Boston, Massachusetts 02115,USA. jrstone@partners.org<br /><br />Hydrogen peroxide (H2O2) is a recently recognized second messenger, which<br />regulates mammalian cell proliferation and migration. The biochemical mechanisms <br />by which mammalian cells sense and respond to low concentrations of H2O2 are<br />poorly understood. Recently, heterogeneous nuclear ribonucleoprotein C1/C2<br />(hnRNP-C1/C2) was found to be rapidly phosphorylated in response to the<br />application of low concentrations of H2O2 to human endothelial cells. Here, using<br />tandem mass spectrometry, four sites of phosphorylation are identified in<br />hnRNP-C1/C2, all of which are in the acidic C-terminal domain of the protein.<br />Under resting conditions, the protein is phosphorylated at S247 and S286. In<br />response to low concentrations of H2O2, there is increased phosphorylation at<br />S240 and at one of the four contiguous serine residues from S225-S228. Studies<br />using a recombinant acidic C-terminal domain of hnRNP-C overexpressed in<br />Escherichia coli demonstrate that protein kinase CK2 phosphorylates hnRNP-C1/C2<br />at S247, while protein kinase A and several protein kinase C isoforms fail to<br />phosphorylate the isolated domain. These findings demonstrate that the acidic<br />C-terminal domain of hnRNP-C1/C2 serves as the site for both basal and stimulated<br />phosphorylation, indicating that this domain may play an important role in the<br />regulation of mRNA binding by hnRNP-C1/C2.<br /><br />PMID: 12564933 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16807684\">PubMed</a></td>\n <td><br />1. Pituitary. 2006;9(2):109-20.<br /><br />Phosphoproteomic analysis of the human pituitary.<br /><br />Beranova-Giorgianni S(1), Zhao Y, Desiderio DM, Giorgianni F.<br /><br />Author information: <br />(1)Charles B. Stout Neuroscience Mass Spectrometry Laboratory, The University of <br />Tennessee Health Science Center, Memphis, TN 38163, USA.<br /><br />The pituitary is the central endocrine gland that regulates the functions of<br />various target organs in the human body. Because of the pivotal regulatory role<br />of the pituitary, it is essential to define on a global scale the components of<br />the pituitary protein machinery, including a comprehensive characterization of<br />the post-translational modifications of the pituitary proteins. Of particular<br />interest is the examination of the phosphorylation status of the pituitary in<br />health and disease. Towards the goal of global profiling of pituitary protein<br />phosphorylation, we report here the application of the in-gel IEF-LC-MS/MS<br />approach to the study of the pituitary phosphoproteome. The analytical strategy<br />combined isoelectric focusing in immobilized pH gradient strips with immobilized <br />metal ion affinity chromatography and mass spectrometry. With this method, a<br />total of 50 phosphorylation sites were characterized in 26 proteins. Because the <br />investigation involved primary tissue, the findings provide a direct glimpse into<br />the phosphoprotein machinery operating within the human pituitary tissue<br />microenvironment.<br /><br />PMID: 16807684 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18318008\">PubMed</a></td>\n <td><br />1. Proteomics. 2008 Apr;8(7):1346-61. doi: 10.1002/pmic.200700884.<br /><br />Large-scale phosphoproteome analysis of human liver tissue by enrichment and<br />fractionation of phosphopeptides with strong anion exchange chromatography.<br /><br />Han G(1), Ye M, Zhou H, Jiang X, Feng S, Jiang X, Tian R, Wan D, Zou H, Gu J.<br /><br />Author information: <br />(1)National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The<br />Chinese Academy of Sciences, Dalian, China.<br /><br />The mixture of phosphopeptides enriched from proteome samples are very complex.<br />To reduce the complexity it is necessary to fractionate the phosphopeptides.<br />However, conventional enrichment methods typically only enrich phosphopeptides<br />but not fractionate phosphopeptides. In this study, the application of strong<br />anion exchange (SAX) chromatography for enrichment and fractionation of<br />phosphopeptides was presented. It was found that phosphopeptides were highly<br />enriched by SAX and majority of unmodified peptides did not bind onto SAX.<br />Compared with Fe(3+) immobilized metal affinity chromatography (Fe(3+)-IMAC),<br />almost double phosphopeptides were identified from the same sample when only one <br />fraction was generated by SAX. SAX and Fe(3+)-IMAC showed the complementarity in <br />enrichment and identification of phosphopeptides. It was also demonstrated that<br />SAX have the ability to fractionate phosphopeptides under gradient elution based <br />on their different interaction with SAX adsorbent. SAX was further applied to<br />enrich and fractionate phosphopeptides in tryptic digest of proteins extracted<br />from human liver tissue adjacent to tumorous region for phosphoproteome<br />profiling. This resulted in the highly confident identification of 274<br />phosphorylation sites from 305 unique phosphopeptides corresponding to 168<br />proteins at false discovery rate (FDR) of 0.96%.<br /><br />PMID: 18318008 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19367720\">PubMed</a></td>\n <td><br />1. J Proteome Res. 2008 Dec;7(12):5167-76.<br /><br />Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and<br />titanium oxide enrichment.<br /><br />Carrascal M(1), Ovelleiro D, Casas V, Gay M, Abian J.<br /><br />Author information: <br />(1)CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina,<br />Campus UAB, 08193 Bellaterra, Spain. montserrat.carrascal@gmail.com<br /><br />T lymphocytes mediate cellular and humoral defense against foreign bodies or<br />autoantigens. An understanding of T-cell information processing furthers studies <br />of the immunological response. We describe a large-scale phosphorylation analysis<br />of primary T cells using a multidimensional separation strategy, involving<br />preparative SDS-PAGE for prefractionation, in-gel digestion and sequential<br />phosphopeptide enrichment using IMAC and TiO2. A total of 281 phosphorylation<br />sites (197 of high confidence, Ascore > 15), mapping to 204 human gene sequences,<br />were identified by LC-MS(n) analysis in an LTQ linear ion trap. Subsequently, we <br />created the LymPHOS database (http://lymphos.org), which links mass spectrometric<br />peptide information to phosphorylation sites and phosphoprotein sequences.<br /><br />PMID: 19367720 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P07910</h1><br><h2>HNRNPC HNRPC</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 306</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18318008\">PubMed</a></td>\n <td><br />1. Proteomics. 2008 Apr;8(7):1346-61. doi: 10.1002/pmic.200700884.<br /><br />Large-scale phosphoproteome analysis of human liver tissue by enrichment and<br />fractionation of phosphopeptides with strong anion exchange chromatography.<br /><br />Han G(1), Ye M, Zhou H, Jiang X, Feng S, Jiang X, Tian R, Wan D, Zou H, Gu J.<br /><br />Author information: <br />(1)National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The<br />Chinese Academy of Sciences, Dalian, China.<br /><br />The mixture of phosphopeptides enriched from proteome samples are very complex.<br />To reduce the complexity it is necessary to fractionate the phosphopeptides.<br />However, conventional enrichment methods typically only enrich phosphopeptides<br />but not fractionate phosphopeptides. In this study, the application of strong<br />anion exchange (SAX) chromatography for enrichment and fractionation of<br />phosphopeptides was presented. It was found that phosphopeptides were highly<br />enriched by SAX and majority of unmodified peptides did not bind onto SAX.<br />Compared with Fe(3+) immobilized metal affinity chromatography (Fe(3+)-IMAC),<br />almost double phosphopeptides were identified from the same sample when only one <br />fraction was generated by SAX. SAX and Fe(3+)-IMAC showed the complementarity in <br />enrichment and identification of phosphopeptides. It was also demonstrated that<br />SAX have the ability to fractionate phosphopeptides under gradient elution based <br />on their different interaction with SAX adsorbent. SAX was further applied to<br />enrich and fractionate phosphopeptides in tryptic digest of proteins extracted<br />from human liver tissue adjacent to tumorous region for phosphoproteome<br />profiling. This resulted in the highly confident identification of 274<br />phosphorylation sites from 305 unique phosphopeptides corresponding to 168<br />proteins at false discovery rate (FDR) of 0.96%.<br /><br />PMID: 18318008 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q1KMD3</h1><br><h2>HNRNPUL2 HNRPUL2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 161</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td>UniProtKB:Q00PI9</td>\n <td></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q1KMD3</h1><br><h2>HNRNPUL2 HNRPUL2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 228</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td>PROSITE-ProRule:PRU00186</td>\n <td></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q01130</h1><br><h2>SRSF2 SFRS2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 2</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q01130</h1><br><h2>SRSF2 SFRS2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 26</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q01130</h1><br><h2>SRSF2 SFRS2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 189</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q01130</h1><br><h2>SRSF2 SFRS2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 191</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q01130</h1><br><h2>SRSF2 SFRS2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 204</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q01130</h1><br><h2>SRSF2 SFRS2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 206</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16964243\">PubMed</a></td>\n <td><br />1. Nat Biotechnol. 2006 Oct;24(10):1285-92. Epub 2006 Sep 10.<br /><br />A probability-based approach for high-throughput protein phosphorylation analysis<br />and site localization.<br /><br />Beausoleil SA(1), Vill\u00e9n J, Gerber SA, Rush J, Gygi SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston,<br />Massachusetts 02115, USA.<br /><br />Comment in<br /> Nat Biotechnol. 2006 Oct;24(10):1226-7.<br /><br />Data analysis and interpretation remain major logistical challenges when<br />attempting to identify large numbers of protein phosphorylation sites by<br />nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS)<br />(Supplementary Figure 1 online). In this report we address challenges that are<br />often only addressable by laborious manual validation, including data set error, <br />data set sensitivity and phosphorylation site localization. We provide a<br />large-scale phosphorylation data set with a measured error rate as determined by <br />the target-decoy approach, we demonstrate an approach to maximize data set<br />sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs),<br />and we present a probability-based score, the Ascore, that measures the<br />probability of correct phosphorylation site localization based on the presence<br />and intensity of site-determining ions in MS/MS spectra. We applied our methods<br />in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we<br />identified 1,761 nonredundant phosphorylation sites from 491 proteins with a<br />peptide false-positive rate of 1.3%.<br /><br />PMID: 16964243 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q01130</h1><br><h2>SRSF2 SFRS2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 208</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/16964243\">PubMed</a></td>\n <td><br />1. Nat Biotechnol. 2006 Oct;24(10):1285-92. Epub 2006 Sep 10.<br /><br />A probability-based approach for high-throughput protein phosphorylation analysis<br />and site localization.<br /><br />Beausoleil SA(1), Vill\u00e9n J, Gerber SA, Rush J, Gygi SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston,<br />Massachusetts 02115, USA.<br /><br />Comment in<br /> Nat Biotechnol. 2006 Oct;24(10):1226-7.<br /><br />Data analysis and interpretation remain major logistical challenges when<br />attempting to identify large numbers of protein phosphorylation sites by<br />nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS)<br />(Supplementary Figure 1 online). In this report we address challenges that are<br />often only addressable by laborious manual validation, including data set error, <br />data set sensitivity and phosphorylation site localization. We provide a<br />large-scale phosphorylation data set with a measured error rate as determined by <br />the target-decoy approach, we demonstrate an approach to maximize data set<br />sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs),<br />and we present a probability-based score, the Ascore, that measures the<br />probability of correct phosphorylation site localization based on the presence<br />and intensity of site-determining ions in MS/MS spectra. We applied our methods<br />in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we<br />identified 1,761 nonredundant phosphorylation sites from 491 proteins with a<br />peptide false-positive rate of 1.3%.<br /><br />PMID: 16964243 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q01130</h1><br><h2>SRSF2 SFRS2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 212</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q01130</h1><br><h2>SRSF2 SFRS2</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 220</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q00839</h1><br><h2>HNRNPU HNRPU SAFA U21.1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 4</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q00839</h1><br><h2>HNRNPU HNRPU SAFA U21.1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 59</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18220336\">PubMed</a></td>\n <td><br />1. J Proteome Res. 2008 Mar;7(3):1346-51. doi: 10.1021/pr0705441. Epub 2008 Jan 26.<br /><br />Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient<br />phosphoproteomic analysis.<br /><br />Cantin GT(1), Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd.<br /><br />Author information: <br />(1)Departments of Cell Biology, The Scripps Research Institute, 10550 North<br />Torrey Pines Road, La Jolla, California 92037, USA.<br /><br />Immobilized metal affinity chromatography (IMAC) is a common strategy used for<br />the enrichment of phosphopeptides from digested protein mixtures. However, this<br />strategy by itself is inefficient when analyzing complex protein mixtures. Here, <br />we assess the effectiveness of using protein-based IMAC as a pre-enrichment step <br />prior to peptide-based IMAC. Ultimately, we couple the two IMAC-based enrichments<br />and MudPIT in a quantitative phosphoproteomic analysis of the epidermal growth<br />factor pathway in mammalian cells identifying 4470 unique phosphopeptides<br />containing 4729 phosphorylation sites.<br /><br />PMID: 18220336 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q00839</h1><br><h2>HNRNPU HNRPU SAFA U21.1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 66</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18220336\">PubMed</a></td>\n <td><br />1. J Proteome Res. 2008 Mar;7(3):1346-51. doi: 10.1021/pr0705441. Epub 2008 Jan 26.<br /><br />Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient<br />phosphoproteomic analysis.<br /><br />Cantin GT(1), Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd.<br /><br />Author information: <br />(1)Departments of Cell Biology, The Scripps Research Institute, 10550 North<br />Torrey Pines Road, La Jolla, California 92037, USA.<br /><br />Immobilized metal affinity chromatography (IMAC) is a common strategy used for<br />the enrichment of phosphopeptides from digested protein mixtures. However, this<br />strategy by itself is inefficient when analyzing complex protein mixtures. Here, <br />we assess the effectiveness of using protein-based IMAC as a pre-enrichment step <br />prior to peptide-based IMAC. Ultimately, we couple the two IMAC-based enrichments<br />and MudPIT in a quantitative phosphoproteomic analysis of the epidermal growth<br />factor pathway in mammalian cells identifying 4470 unique phosphopeptides<br />containing 4729 phosphorylation sites.<br /><br />PMID: 18220336 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q00839</h1><br><h2>HNRNPU HNRPU SAFA U21.1</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 271</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17487921\">PubMed</a></td>\n <td><br />1. Electrophoresis. 2007 Jun;28(12):2027-34.<br /><br />Toward a global characterization of the phosphoproteome in prostate cancer cells:<br />identification of phosphoproteins in the LNCaP cell line.<br /><br />Giorgianni F(1), Zhao Y, Desiderio DM, Beranova-Giorgianni S.<br /><br />Author information: <br />(1)Charles B. Stout Neuroscience Mass Spectrometry Laboratory, University of<br />Tennessee Health Science Center, Memphis, TN, USA.<br /><br />Protein phosphorylation plays a major role in most cell-signaling pathways in all<br />eukaryotic cells. Disruptions in phosphorylation-mediated cell-signaling events<br />are associated with various diseases, including cancer. Here, we applied a fully <br />non-gel-based methodology to obtain an initial panel of phosphoproteins from the <br />LNCaP human prostate cancer cell line. The analytical strategy involved<br />enrichment of phosphopeptides by immobilized metal ion affinity chromatography,<br />the use of POROS Oligo R3 to capture phosphopeptides that were not retained with <br />a C18 packing, and gas-phase fractionation in the m/z dimension to extend the<br />dynamic range of the LC-MS/MS analysis. In this pilot investigation, 137<br />phosphorylation sites in 81 phosphoproteins were identified. The characterized<br />phosphoproteins include kinases, co-regulators of steroid receptors, and a number<br />of cancer-related proteins.<br /><br />PMID: 17487921 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P51991</h1><br><h2>HNRNPA3 HNRPA3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 14</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P51991</h1><br><h2>HNRNPA3 HNRPA3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 43</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P51991</h1><br><h2>HNRNPA3 HNRPA3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 116</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P51991</h1><br><h2>HNRNPA3 HNRPA3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 350</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P51991</h1><br><h2>HNRNPA3 HNRPA3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 358</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P51991</h1><br><h2>HNRNPA3 HNRPA3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 366</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>P51991</h1><br><h2>HNRNPA3 HNRPA3</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 370</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13247</h1><br><h2>SRSF6 SFRS6 SRP55</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 45</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/24275569\">PubMed</a></td>\n <td><br />1. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 <br />Nov 22.<br /><br />An enzyme assisted RP-RPLC approach for in-depth analysis of human liver<br />phosphoproteome.<br /><br />Bian Y(1), Song C(1), Cheng K(1), Dong M(1), Wang F(2), Huang J(1), Sun D(3),<br />Wang L(3), Ye M(4), Zou H(5).<br /><br />Author information: <br />(1)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences,<br />Beijing 100049, China. (2)Key Laboratory of Separation Sciences for Analytical<br />Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical<br />Physics, Chinese Academy of Sciences, Dalian 116023, China. (3)The Second<br />Affiliated Hospital of Dalian Medical University, Dalian 116027, China. (4)Key<br />Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: mingliang@dicp.ac.cn.<br />(5)Key Laboratory of Separation Sciences for Analytical Chemistry, National<br />Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy<br />of Sciences, Dalian 116023, China. Electronic address: hanfazou@dicp.ac.cn.<br /><br />Protein phosphorylation is one of the most common post-translational<br />modifications. It plays key roles in regulating diverse biological processes of<br />liver tissues. To better understand the role of protein phosphorylation in liver <br />functions, it is essential to perform in-depth phosphoproteome analysis of human <br />liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid<br />chromatography (RP-RPLC) approach with both RPLC separations operated with<br />optimized acidic mobile phase was developed. High orthogonal separation was<br />achieved by trypsin digestion of the Glu-C generated peptides in the fractions<br />collected from the first RPLC separation. The phosphoproteome coverage was<br />further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ<br />Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526<br />nonredundant phosphoproteins were finally identified from normal human liver<br />tissues. Of these sites, 15,229 sites were confidently localized with Ascore\u226513. <br />This dataset was the largest phosphoproteome dataset of human liver. It can be a <br />public resource for the liver research community and holds promise for further<br />biology studies.BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the<br />two RPLC separations operated both with optimized acidic mobile phases. The<br />identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. <br />The largest phosphoproteome dataset of human liver was generated.<br /><br />Copyright \u00a9 2013 Elsevier B.V. All rights reserved.<br /><br />PMID: 24275569 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13247</h1><br><h2>SRSF6 SFRS6 SRP55</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 81</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13247</h1><br><h2>SRSF6 SFRS6 SRP55</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 84</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13247</h1><br><h2>SRSF6 SFRS6 SRP55</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 299</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13247</h1><br><h2>SRSF6 SFRS6 SRP55</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 303</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/18669648\">PubMed</a></td>\n <td><br />1. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi:<br />10.1073/pnas.0805139105. Epub 2008 Jul 31.<br /><br />A quantitative atlas of mitotic phosphorylation.<br /><br />Dephoure N(1), Zhou C, Vill\u00e9n J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi<br />SP.<br /><br />Author information: <br />(1)Department of Cell Biology, Harvard University Medical School, 240 Longwood<br />Avenue, Boston, MA 02115, USA.<br /><br />The eukaryotic cell division cycle is characterized by a sequence of orderly and <br />highly regulated events resulting in the duplication and separation of all<br />cellular material into two newly formed daughter cells. Protein phosphorylation<br />by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight<br />into how phosphorylation regulates the cell cycle, we sought to identify proteins<br />whose phosphorylation is cell cycle regulated. Using stable isotope labeling<br />along with a two-step strategy for phosphopeptide enrichment and high mass<br />accuracy mass spectrometry, we examined protein phosphorylation in a human cell<br />line arrested in the G(1) and mitotic phases of the cell cycle. We report the<br />identification of >14,000 different phosphorylation events, more than half of<br />which, to our knowledge, have not been described in the literature, along with<br />relative quantitative data for the majority of these sites. We observed >1,000<br />proteins with increased phosphorylation in mitosis including many known cell<br />cycle regulators. The majority of sites on regulated phosphopeptides lie in<br />[S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of<br />the proteins may be CDK substrates. Analysis of non-proline site-containing<br />phosphopeptides identified two unique motifs that suggest there are at least two <br />undiscovered mitotic kinases.<br /><br />PMCID: PMC2504835<br />PMID: 18669648 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/19690332\">PubMed</a></td>\n <td><br />1. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.<br /><br />Quantitative phosphoproteomic analysis of T cell receptor signaling reveals<br />system-wide modulation of protein-protein interactions.<br /><br />Mayya V(1), Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.<br /><br />Author information: <br />(1)Department of Cell Biology, University of Connecticut Health Center,<br />Farmington, 06030, USA.<br /><br />Protein phosphorylation events during T cell receptor (TCR) signaling control the<br />formation of complexes among proteins proximal to the TCR, the activation of<br />kinase cascades, and the activation of transcription factors; however, the mode<br />and extent of the influence of phosphorylation in coordinating the diverse<br />phenomena associated with T cell activation are unclear. Therefore, we used the<br />human Jurkat T cell leukemia cell line as a model system and performed<br />large-scale quantitative phosphoproteomic analyses of TCR signaling. We<br />identified 10,665 unique phosphorylation sites, of which 696 showed<br />TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation <br />data sets to uncover underlying mechanisms associated with T cell activation. We <br />found that, upon stimulation of the TCR, phosphorylation events extensively<br />targeted protein modules involved in all of the salient phenomena associated with<br />T cell activation: patterning of surface proteins, endocytosis of the TCR,<br />formation of the F-actin cup, inside-out activation of integrins, polarization of<br />microtubules, production of cytokines, and alternative splicing of messenger RNA.<br />Further, case-by-case analysis of TCR-responsive phosphorylation sites on<br />proteins belonging to relevant functional modules together with network analysis <br />allowed us to deduce that serine-threonine (S-T) phosphorylation modulated<br />protein-protein interactions (PPIs) in a system-wide fashion. We also provide<br />experimental support for this inference by showing that phosphorylation of<br />tubulin on six distinct serine residues abrogated PPIs during the assembly of<br />microtubules. We propose that modulation of PPIs by stimulus-dependent changes in<br />S-T phosphorylation state is a widespread phenomenon applicable to many other<br />signaling systems.<br /><br />PMID: 19690332 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/22767602\">PubMed</a></td>\n <td><br />1. J Biol Chem. 2012 Aug 31;287(36):30497-506. doi: 10.1074/jbc.M112.355412. Epub<br />2012 Jul 5.<br /><br />Dual-specificity tyrosine phosphorylation-regulated kinase 1A (Dyrk1A) modulates <br />serine/arginine-rich protein 55 (SRp55)-promoted Tau exon 10 inclusion.<br /><br />Yin X(1), Jin N, Gu J, Shi J, Zhou J, Gong CX, Iqbal K, Grundke-Iqbal I, Liu F.<br /><br />Author information: <br />(1)Jiangsu Key Laboratory of Neuroregeneration, Medical School, Nantong<br />University, Nantong, Jiangsu, 226001, China.<br /><br />Tau exon 10, which encodes the second microtubule-binding repeat, is regulated by<br />alternative splicing. Its alternative splicing generates Tau isoforms with three-<br />or four-microtubule-binding repeats, named 3R-tau and 4R-tau. Adult human brain<br />expresses equal levels of 3R-tau and 4R-tau. Imbalance of 3R-tau and 4R-tau<br />causes Tau aggregation and neurofibrillary degeneration. In the present study, we<br />found that splicing factor SRp55 (serine/arginine-rich protein 55) promoted Tau<br />exon 10 inclusion. Knockdown of SRp55 significantly promoted Tau exon 10<br />exclusion. The promotion of Tau exon 10 inclusion by SRp55 required the<br />arginine/serine-rich region, which was responsible for the subnucleic speckle<br />localization. Dyrk1A (dual specificity tyrosine-phosphorylated and regulated<br />kinase 1A) interacted with SRp55 and mainly phosphorylated its proline-rich<br />domain. Phosphorylation of SRp55 by Dyrk1A suppressed its ability to promote Tau <br />exon 10 inclusion. Up-regulation of Dyrk1A as in Down syndrome could lead to<br />neurofibrillary degeneration by shifting the alternative splicing of Tau exon 10 <br />to an increase in the ratio of 3R-tau/4R-tau.<br /><br />PMCID: PMC3436298<br />PMID: 22767602 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13247</h1><br><h2>SRSF6 SFRS6 SRP55</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 314</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13247</h1><br><h2>SRSF6 SFRS6 SRP55</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 316</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/17081983\">PubMed</a></td>\n <td><br />1. Cell. 2006 Nov 3;127(3):635-48.<br /><br />Global, in vivo, and site-specific phosphorylation dynamics in signaling<br />networks.<br /><br />Olsen JV(1), Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.<br /><br />Cell signaling mechanisms often transmit information via posttranslational<br />protein modifications, most importantly reversible protein phosphorylation. Here <br />we develop and apply a general mass spectrometric technology for identification<br />and quantitation of phosphorylation sites as a function of stimulus, time, and<br />subcellular location. We have detected 6,600 phosphorylation sites on 2,244<br />proteins and have determined their temporal dynamics after stimulating HeLa cells<br />with epidermal growth factor (EGF) and recorded them in the Phosida database.<br />Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF,<br />and these were classified by their temporal profiles. Surprisingly, a majority of<br />proteins contain multiple phosphorylation sites showing different kinetics,<br />suggesting that they serve as platforms for integrating signals. In addition to<br />protein kinase cascades, the targets of reversible phosphorylation include<br />ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different<br />transcriptional regulators. The dynamic phosphoproteome provides a missing link<br />in a global, integrative view of cellular regulation.<br /><br />PMID: 17081983 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/20068231\">PubMed</a></td>\n <td><br />1. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.<br /><br />Quantitative phosphoproteomics reveals widespread full phosphorylation site<br />occupancy during mitosis.<br /><br />Olsen JV(1), Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F,<br />Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.<br /><br />Author information: <br />(1)Department of Proteomics and Signal Transduction, Max-Planck-Institute for<br />Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.<br /><br />Eukaryotic cells replicate by a complex series of evolutionarily conserved events<br />that are tightly regulated at defined stages of the cell division cycle.<br />Progression through this cycle involves a large number of dedicated protein<br />complexes and signaling pathways, and deregulation of this process is implicated <br />in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics<br />to investigate the proteome and phosphoproteome of the human cell cycle on a<br />global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites<br />and their dynamics. Co-regulated proteins and phosphorylation sites were grouped <br />according to their cell cycle kinetics and compared to publicly available<br />messenger RNA microarray data. Most detected phosphorylation sites and more than <br />20% of all quantified proteins showed substantial regulation, mainly in mitotic<br />cells. Kinase-motif analysis revealed global activation during S phase of the DNA<br />damage response network, which was mediated by phosphorylation by ATM or ATR or<br />DNA-dependent protein kinases. We determined site-specific stoichiometry of more <br />than 5000 sites and found that most of the up-regulated sites phosphorylated by<br />cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in<br />mitotic cells. In particular, nuclear proteins and proteins involved in<br />regulating metabolic processes have high phosphorylation site occupancy in<br />mitosis. This suggests that these proteins may be inactivated by phosphorylation <br />in mitotic cells.<br /><br />PMID: 20068231 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13243</h1><br><h2>SRSF5 HRS SFRS5 SRP40</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 227</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13243</h1><br><h2>SRSF5 HRS SFRS5 SRP40</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 229</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <td><a href=\"http://ncbi.nlm.nih.gov/pubmed/21406692\">PubMed</a></td>\n <td><br />1. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.<br /><br />System-wide temporal characterization of the proteome and phosphoproteome of<br />human embryonic stem cell differentiation.<br /><br />Rigbolt KT(1), Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova<br />I, Kassem M, Mann M, Olsen JV, Blagoev B.<br /><br />Author information: <br />(1)Center for Experimental BioInformatics, Department of Biochemistry and<br />Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense<br />M, Denmark.<br /><br />To elucidate cellular events underlying the pluripotency of human embryonic stem <br />cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic <br />analyses of hESCs during differentiation initiated by a diacylglycerol analog or <br />transfer to media that had not been conditioned by feeder cells. We profiled 6521<br />proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic <br />changes in phosphorylation status during 24 hours of differentiation. These data <br />are a resource for studies of the events associated with the maintenance of hESC <br />pluripotency and those accompanying their differentiation. From these data, we<br />identified a core hESC phosphoproteome of sites with similar robust changes in<br />response to the two distinct treatments. These sites exhibited distinct dynamic<br />phosphorylation patterns, which were linked to known or predicted kinases on the <br />basis of the matching sequence motif. In addition to identifying previously<br />unknown phosphorylation sites on factors associated with differentiation, such as<br />kinases and transcription factors, we observed dynamic phosphorylation of DNA<br />methyltransferases (DNMTs). We found a specific interaction of DNMTs during early<br />differentiation with the PAF1 (polymerase-associated factor 1) transcriptional<br />elongation complex, which binds to promoters of the pluripotency and known DNMT<br />target genes encoding OCT4 and NANOG, thereby providing a possible molecular link<br />for the silencing of these genes during differentiation.<br /><br />PMID: 21406692 [PubMed - indexed for MEDLINE]<br /><br /></td>\n </tr>\n </tbody>\n</table>", "<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\"><h1>Q13243</h1><br><h2>SRSF5 HRS SFRS5 SRP40</h2><br><h2>Phosphorylation : Phosphoserine</h2><br><h3>AA position: 233</h3><br><table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th>Source</th>\n <th>Information</th>\n </
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