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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.4" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_4.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="1.10.0" type="string" description="" /> | |
| <ITEM name="num_vertices" value="15" type="int" description="" /> | |
| <ITEM name="num_edges" value="14" type="int" description="" /> | |
| <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> | |
| <html><head><meta name="qrichtext" content="1" /><style type="text/css"> | |
| p, li { white-space: pre-wrap; } | |
| </style></head><body style=" font-family:'Arial'; font-size:12pt; font-weight:400; font-style:normal;"> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Workflow for label-free quantification as published in Weisser et al., J. Proteome Res. (2013) (DOI: 10.1021/pr300992u). Updated for OpenMS 1.10.</span></p> | |
| <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Inputs (n samples):</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">1: raw data in profile mode (n mzML files)</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">2: corresponding peptide/protein identification data (n idXML files)</span></p> | |
| <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Outputs:</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">7: annotated feature maps (n featureXML files)</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">11: RT transformation descriptions (n trafoXML files)</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">12: annotated consensus map (1 consensusXML file)</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">14: table of peptide abundances (1 CSV file)</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">15: table of protein abundances (1 CSV file)</span></p> | |
| <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Parameters (compare Supplemental Table S2 in the publication):</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">FeatureFinderCentroided: set &quot;algorithm:mass_trace:mz_tolerance&quot; and &quot;algorithm:isotopic_pattern:mz_tolerance&quot; according to your instrument</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">IDFilter: adjust &quot;score:pep&quot; according to your ID results and desired FDR</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">MapAlignerIdentification: increase &quot;algorithm:min_run_occur&quot; for a more reliable alignment (e.g. to half the number of samples)</span></p></body></html>]]>" type="string" description="" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" /> | |
| <ITEMLIST name="file_names" type="string" description=""> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-360" type="float" description="" /> | |
| <ITEM name="y_pos" value="-360" type="float" description="" /> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="IDFilter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-180" type="float" description="" /> | |
| <ITEM name="y_pos" value="-220" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file " tags="input file,required" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="string" description="output file " tags="output file,required" supported_formats="*.idXML" /> | |
| <ITEM name="min_length" value="0" type="int" description="Keep only peptide hits with a length greater or equal this value." restrictions="0:" /> | |
| <ITEM name="unique" value="false" type="string" description="If a peptide hit occurs more than once, only one instance is kept. This will (for instance) remove redundant identifications from multiple charge states or concurrent CID+HCD spectra. If you are aiming towards quantitation, you probably do *not* want to use this flag!" restrictions="true,false" /> | |
| <ITEM name="unique_per_protein" value="false" type="string" description="Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="score" description="Filtering by peptide/protein score"> | |
| <ITEM name="pep" value="0" type="float" description="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc." /> | |
| <ITEM name="prot" value="0" type="float" description="The score which should be reached by a protein hit to be kept." /> | |
| </NODE> | |
| <NODE name="thresh" description="Filtering by significance threshold"> | |
| <ITEM name="pep" value="0" type="float" description="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." /> | |
| <ITEM name="prot" value="0" type="float" description="Keep a protein hit only if its score is above this fraction of the protein significance threshold." /> | |
| </NODE> | |
| <NODE name="whitelist" description="Filtering by whitelisting (only instances also present in a whitelist file can pass)"> | |
| <ITEM name="proteins" value="" type="string" description="filename of a FASTA file containing protein sequences.#br#All peptides that are not a substring of a sequence in this file are removed#br#All proteins whose accession is not present in this file are removed." tags="input file" supported_formats="*.FASTA" /> | |
| <ITEM name="by_seq_only" value="false" type="string" description="Match peptides with FASTA file by sequence instead of accession and disable protein filtering." restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="blacklist" description="Filtering by blacklisting (only instances not present in a blacklist file can pass)"> | |
| <ITEM name="peptides" value="" type="string" description="Peptides having the same sequence as any peptide in this file will be filtered out#br#" tags="input file" supported_formats="*.idXML" /> | |
| </NODE> | |
| <NODE name="rt" description="Filtering by RT predicted by 'RTPredict'"> | |
| <ITEM name="p_value" value="0" type="float" description="Retention time filtering by the p-value predicted by RTPredict." restrictions="0:1" /> | |
| <ITEM name="p_value_1st_dim" value="0" type="float" description="Retention time filtering by the p-value predicted by RTPredict for first dimension." restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="best" description="Filtering best hits per spectrum (for peptides) or from proteins"> | |
| <ITEM name="n_peptide_hits" value="0" type="int" description="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0)." restrictions="0:" /> | |
| <ITEM name="n_protein_hits" value="0" type="int" description="Keep only the 'n' highest scoring protein hits (for n>0)." restrictions="0:" /> | |
| <ITEM name="strict" value="true" type="string" description="Keep only the highest scoring peptide hit.#br#Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept." restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="PeakPickerHiRes" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-360" type="float" description="" /> | |
| <ITEM name="y_pos" value="-220" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input profile data file " tags="input file,required" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="string" description="output peak file " tags="output file,required" supported_formats="*.mzML" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="signal_to_noise" value="0" type="float" description="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" restrictions="0:" /> | |
| <ITEM name="ms1_only" value="true" type="string" description="If true, peak picking is only applied to MS1 scans. Other scans are copied to the output without changes." restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FeatureFinderCentroided" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-360" type="float" description="" /> | |
| <ITEM name="y_pos" value="-60" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file" tags="input file,required" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="string" description="output file" tags="output file,required" supported_formats="*.featureXML" /> | |
| <ITEM name="seeds" value="" type="string" description="User specified seed list" tags="input file" supported_formats="*.featureXML" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Algorithm section"> | |
| <ITEM name="debug" value="false" type="string" description="When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode)." restrictions="true,false" /> | |
| <NODE name="intensity" description="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)"> | |
| <ITEM name="bins" value="10" type="int" description="Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.#br#This parameter should be decreased, if the algorithm is used on small regions of a map." restrictions="1:" /> | |
| </NODE> | |
| <NODE name="mass_trace" description="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1)."> | |
| <ITEM name="mz_tolerance" value="0.01" type="float" description="Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instument.#br#This value must be smaller than that 1/charge_high!" restrictions="0:" /> | |
| <ITEM name="min_spectra" value="8" type="int" description="Number of spectra that have to show a similar peak mass in a mass trace." restrictions="1:" /> | |
| <ITEM name="max_missing" value="2" type="int" description="Number of consecutive spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below 'min_spectra'!" restrictions="0:" /> | |
| <ITEM name="slope_bound" value="1" type="float" description="The maximum slope of mass trace intensities when extending from the highest peak.#br#This parameter is important to seperate overlapping elution peaks.#br#It should be increased if feature elution profiles fluctuate a lot." restrictions="0:" /> | |
| </NODE> | |
| <NODE name="isotopic_pattern" description="Settings for the calculation of a score indicating if a peak is part of a isotoipic pattern (between 0 and 1)."> | |
| <ITEM name="charge_low" value="2" type="int" description="Lowest charge to search for." restrictions="1:" /> | |
| <ITEM name="charge_high" value="6" type="int" description="Highest charge to search for." restrictions="1:" /> | |
| <ITEM name="mz_tolerance" value="0.01" type="float" description="Tolerated m/z deviation from the theoretical isotopic pattern.#br#It should be larger than the m/z resolution of the instument.#br#This value must be smaller than that 1/charge_high!" restrictions="0:" /> | |
| <ITEM name="intensity_percentage" value="10" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present." tags="advanced" restrictions="0:100" /> | |
| <ITEM name="intensity_percentage_optional" value="0.1" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing." tags="advanced" restrictions="0:100" /> | |
| <ITEM name="optional_fit_improvement" value="2" type="float" description="Minimal percental improvement of isotope fit to allow leaving out an optional peak." tags="advanced" restrictions="0:100" /> | |
| <ITEM name="mass_window_width" value="25" type="float" description="Window width in Dalton for precalculation of estimated isotope distribtions." tags="advanced" restrictions="1:200" /> | |
| </NODE> | |
| <NODE name="seed" description="Settings that determine which peaks are considered a seed"> | |
| <ITEM name="min_score" value="0.5" type="float" description="Minimum seed score a peak has to reach to be used as seed.#br#The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.#br#If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score." restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="fit" description="Settings for the model fitting"> | |
| <ITEM name="epsilon_abs" value="0.0001" type="float" description="Absolute epsilon used for convergence of the fit." tags="advanced" restrictions="0:" /> | |
| <ITEM name="epsilon_rel" value="0.0001" type="float" description="Relative epsilon used for convergence of the fit." tags="advanced" restrictions="0:" /> | |
| <ITEM name="max_iterations" value="500" type="int" description="Maximum number of iterations of the fit." tags="advanced" restrictions="1:" /> | |
| </NODE> | |
| <NODE name="feature" description="Settings for the features (intensity, quality assessment, ...)"> | |
| <ITEM name="min_score" value="0.5" type="float" description="Feature score threshold for a feature to be reported.#br#The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks." restrictions="0:1" /> | |
| <ITEM name="min_isotope_fit" value="0.6" type="float" description="Minimum isotope fit of the feature before model fitting." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="min_trace_score" value="0.4" type="float" description="Trace score threshold.#br#Traces below this threshold are removed after the model fitting.#br#This parameter is important for features that overlap in m/z dimension." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="min_rt_span" value="0.333" type="float" description="Minimum RT span in relation to extended area that has to remain after model fitting." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="max_rt_span" value="2.5" type="float" description="Maximum RT span in relation to extended area that the model is allowed to have." tags="advanced" restrictions="0.5:" /> | |
| <ITEM name="rt_shape" value="symmetric" type="string" description="Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used." tags="advanced" restrictions="symmetric,asymmetric" /> | |
| <ITEM name="max_intersection" value="0.35" type="float" description="Maximum allowed intersection of features." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="reported_mz" value="monoisotopic" type="string" description="The mass type that is reported for features.#br#'maximum' returns the m/z value of the highest mass trace.#br#'average' returns the intensity-weighted average m/z value of all contained peaks.#br#'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model." restrictions="maximum,average,monoisotopic" /> | |
| </NODE> | |
| <NODE name="user-seed" description="Settings for user-specified seeds."> | |
| <ITEM name="rt_tolerance" value="30" type="float" description="Allowed RT deviation of seeds from the user-specified seed position." restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="0.1" type="float" description="Allowed m/z deviation of seeds from the user-specified seed position." restrictions="0:" /> | |
| <ITEM name="min_score" value="0.5" type="float" description="Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case." restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="debug" description=""> | |
| <ITEM name="pseudo_rt_shift" value="500" type="float" description="Pseudo RT shift used when ." tags="advanced" restrictions="1:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="MapAlignerIdentification" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="120" type="float" description="" /> | |
| <ITEM name="y_pos" value="-60" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="string" description="Input files separated by blanks (all must have the same file type)" tags="input file,required" supported_formats="*.featureXML,*.consensusXML,*.idXML"> | |
| </ITEMLIST> | |
| <ITEMLIST name="out" type="string" description="Output files separated by blanks" tags="output file" supported_formats="*.featureXML,*.consensusXML,*.idXML"> | |
| </ITEMLIST> | |
| <ITEMLIST name="trafo_out" type="string" description="Transformation output files separated by blanks" tags="output file" supported_formats="*.trafoXML"> | |
| </ITEMLIST> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="reference" description="Options to define a reference file"> | |
| <ITEM name="file" value="" type="string" description="File to use as reference" tags="input file" supported_formats="*.featureXML,*.consensusXML,*.idXML" /> | |
| <ITEM name="index" value="0" type="int" description="Use one of the input files as reference ('1' for the first file, etc.).#br#If '0', no explicit reference is set - the algorithm will use an average of all inputs as reference." restrictions="0:" /> | |
| </NODE> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="peptide_score_threshold" value="0" type="float" description="Score threshold for peptide hits to be used in the alignment.#br#Select a value that allows only 'high confidence' matches." /> | |
| <ITEM name="min_run_occur" value="2" type="int" description="Minimum number of runs (incl. reference, if any) a peptide must occur in to be used for the alignment.#br#Unless you have very few runs or identifications, increase this value to focus on more informative peptides." restrictions="2:" /> | |
| <ITEM name="max_rt_shift" value="0.5" type="float" description="Maximum realistic RT difference for a peptide (median per run vs. reference). Peptides with higher shifts (outliers) are not used to compute the alignment.#br#If 0, no limit (disable filter); if > 1, the final value in seconds; if <= 1, taken as a fraction of the range of the reference RT scale." restrictions="0:" /> | |
| <ITEM name="use_unassigned_peptides" value="true" type="string" description="Should unassigned peptide identifications be used when computing an alignment of feature maps? If 'false', only peptide IDs assigned to features will be used." restrictions="true,false" /> | |
| <ITEM name="use_feature_rt" value="false" type="string" description="When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to. If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.#br#Precludes 'use_unassigned_peptides'." restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="model" description="Options to control the modeling of retention time transformations from data"> | |
| <ITEM name="type" value="b_spline" type="string" description="Type of model" restrictions="linear,b_spline,interpolated" /> | |
| <NODE name="linear" description="Parameters for 'linear' model"> | |
| <ITEM name="symmetric_regression" value="false" type="string" description="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="b_spline" description="Parameters for 'b_spline' model"> | |
| <ITEM name="num_breakpoints" value="5" type="int" description="Number of breakpoints of the cubic spline in the smoothing step. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape." restrictions="2:" /> | |
| <ITEM name="break_positions" value="uniform" type="string" description="How to distribute the breakpoints on the retention time scale. 'uniform': intervals of equal size; 'quantiles': equal number of data points per interval." restrictions="uniform,quantiles" /> | |
| </NODE> | |
| <NODE name="interpolated" description="Parameters for 'interpolated' model"> | |
| <ITEM name="interpolation_type" value="cspline" type="string" description="Type of interpolation to apply." restrictions="linear,cspline,akima" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="9" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FeatureLinkerUnlabeledQT" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="300" type="float" description="" /> | |
| <ITEM name="y_pos" value="-60" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="string" description="input files separated by blanks" tags="input file,required" supported_formats="*.featureXML,*.consensusXML"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="string" description="Output file" tags="output file,required" supported_formats="*.consensusXML" /> | |
| <ITEM name="keep_subelements" value="false" type="string" description="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="use_identifications" value="true" type="string" description="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." restrictions="true,false" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="Compare features normally even if their charge states are different" restrictions="true,false" /> | |
| <NODE name="distance_RT" description="Distance component based on RT differences"> | |
| <ITEM name="max_difference" value="60" type="float" description="Maximum allowed difference in RT" restrictions="0:" /> | |
| <ITEM name="exponent" value="1" type="float" description="Normalized RT differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="RT distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_MZ" description="Distance component based on m/z differences"> | |
| <ITEM name="max_difference" value="0.02" type="float" description="Maximum allowed difference in m/z (unit defined by 'mz_unit')" restrictions="0:" /> | |
| <ITEM name="unit" value="Da" type="string" description="Unit of the 'max_difference' parameter" restrictions="Da,ppm" /> | |
| <ITEM name="exponent" value="2" type="float" description="Normalized m/z differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="m/z distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_intensity" description="Distance component based on differences in relative intensity"> | |
| <ITEM name="exponent" value="1" type="float" description="Differences in relative intensity are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="0" type="float" description="Distances based on relative intensity are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" /> | |
| <ITEM name="x_pos" value="120" type="float" description="" /> | |
| <ITEM name="y_pos" value="80" type="float" description="" /> | |
| </NODE> | |
| <NODE name="11" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" /> | |
| <ITEM name="x_pos" value="300" type="float" description="" /> | |
| <ITEM name="y_pos" value="80" type="float" description="" /> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" /> | |
| <ITEM name="x_pos" value="-180" type="float" description="" /> | |
| <ITEM name="y_pos" value="80" type="float" description="" /> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" /> | |
| <ITEM name="x_pos" value="-20" type="float" description="" /> | |
| <ITEM name="y_pos" value="-60" type="float" description="" /> | |
| <ITEM name="round_based" value="false" type="string" description="" /> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" /> | |
| <ITEMLIST name="file_names" type="string" description=""> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-180" type="float" description="" /> | |
| <ITEM name="y_pos" value="-360" type="float" description="" /> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" /> | |
| <ITEM name="x_pos" value="480" type="float" description="" /> | |
| <ITEM name="y_pos" value="80" type="float" description="" /> | |
| </NODE> | |
| <NODE name="14" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" /> | |
| <ITEM name="x_pos" value="640" type="float" description="" /> | |
| <ITEM name="y_pos" value="80" type="float" description="" /> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="IDMapper" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-180" type="float" description="" /> | |
| <ITEM name="y_pos" value="-60" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="id" value="" type="string" description="Protein/peptide identifications file" tags="input file,required" supported_formats="*.idXML" /> | |
| <ITEM name="in" value="" type="string" description="Feature map/consensus map file" tags="input file,required" supported_formats="*.featureXML,*.consensusXML,*.mzq" /> | |
| <ITEM name="out" value="" type="string" description="Output file (the format depends on the input file format)." tags="output file,required" supported_formats="*.featureXML,*.consensusXML,*.mzq" /> | |
| <ITEM name="rt_tolerance" value="5" type="float" description="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="40" type="float" description="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." restrictions="0:" /> | |
| <ITEM name="mz_measure" value="ppm" type="string" description="Unit of 'mz_tolerance'." restrictions="ppm,Da" /> | |
| <ITEM name="mz_reference" value="peptide" type="string" description="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)" restrictions="precursor,peptide" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="feature" description="Additional options for featureXML input"> | |
| <ITEM name="use_centroid_rt" value="false" type="string" description="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." restrictions="true,false" /> | |
| <ITEM name="use_centroid_mz" value="true" type="string" description="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.#br#(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="consensusfeature" description="Additional options for consensusXML input"> | |
| <ITEM name="use_subelements" value="false" type="string" description="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="12" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="ProteinQuantifier" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="480" type="float" description="" /> | |
| <ITEM name="y_pos" value="-60" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Input file" tags="input file,required" supported_formats="*.featureXML,*.consensusXML" /> | |
| <ITEM name="protxml" value="" type="string" description="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." tags="input file" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="string" description="Output file for protein abundances" tags="output file" supported_formats="*.csv" /> | |
| <ITEM name="peptide_out" value="" type="string" description="Output file for peptide abundances" tags="output file" supported_formats="*.csv" /> | |
| <ITEM name="mzTab_out" value="" type="string" description="Export to mzTab.#br#Either 'out', 'peptide_out', or 'mzTab_out' are required. They can be used together." tags="output file" supported_formats="*.csv" /> | |
| <ITEM name="top" value="1" type="int" description="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" restrictions="0:" /> | |
| <ITEM name="average" value="median" type="string" description="Averaging method used to compute protein abundances from peptide abundances" restrictions="median,mean,sum" /> | |
| <ITEM name="include_all" value="false" type="string" description="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" restrictions="true,false" /> | |
| <ITEM name="filter_charge" value="false" type="string" description="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." restrictions="true,false" /> | |
| <ITEM name="ratios" value="false" type="string" description="Prints the log2 ratios of the abundance value to the output file. (log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) ....)" restrictions="true,false" /> | |
| <ITEM name="ratiosSILAC" value="false" type="string" description="Prints the SILAC log2 ratios for a triple SILAC experiment to the output file. Only performed if three maps are given, otherwise nothing will be seen in the output file. (log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="consensus" description="Additional options for consensus maps"> | |
| <ITEM name="normalize" value="false" type="string" description="Scale peptide abundances so that medians of all samples are equal" restrictions="true,false" /> | |
| <ITEM name="fix_peptides" value="false" type="string" description="Use the same peptides for protein quantification across all samples.#br#With 'top 0', all peptides that occur in every sample are considered.#br#Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="format" description="Output formatting options"> | |
| <ITEM name="separator" value="," type="string" description="Character(s) used to separate fields; by default, the 'tab' character is used" /> | |
| <ITEM name="quoting" value="double" type="string" description="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" restrictions="none,double,escape" /> | |
| <ITEM name="replacement" value="_" type="string" description="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="edges" description=""> | |
| <NODE name="0" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/2" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="8/9" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="8/10" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="trafo_out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="9/11" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="7/8" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/1" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="3/4" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="4/5" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="id" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="2/5" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="9" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="5/7" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="5/6" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="11" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="9/12" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="12" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="12/13" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="peptide_out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="12/14" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </PARAMETERS> |
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from old website's workflow section:
�Workflow for label-free quantification as published in Weisser et al., J. Proteome Res. (2013) (DOI: 10.1021/pr300992u). Updated for OpenMS 1.10.
Inputs (n samples):
1: raw data in profile mode (n mzML files)
2: corresponding peptide/protein identification data (n idXML files)
Outputs:
7: annotated feature maps (n featureXML files)
11: RT transformation descriptions (n trafoXML files)
12: annotated consensus map (1 consensusXML file)
14: table of peptide abundances (1 CSV file)
15: table of protein abundances (1 CSV file)
Parameters (compare Supplemental Table S2 in the publication):
FeatureFinderCentroided: set "algorithm:mass_trace:mz_tolerance" and "algorithm:isotopic_pattern:mz_tolerance" according to your instrument
IDFilter: adjust "score:pep" according to your ID results and desired FDR
MapAlignerIdentification: increase "algorithm:min_run_occur" for a more reliable alignment (e.g. to half the number of samples)