Here, we describe a mzQC JSON document used for QC of a single mass spectrometry run. Find the complete file at the bottom of this document or in the example folder. The documents main anchor is between the outer curly brackets:
{ "mzQC": {
...
}
An mzQC document is composed by general information about the file,
"creationDate": "2020-12-01T11:56:34",
"version": "1.0.0",
"contactName": "Mathias Walzer",
"contactAddress": "walzer@ebi.ac.uk",
cv term reference information at the bottom,
"controlledVocabularies": [
{
"name": "Proteomics Standards Initiative Quality Control Ontology",
"uri": "https://github.com/HUPO-PSI/qcML-development/blob/master/cv/v0_1_0/qc-cv.obo",
"version": "0.1.0"
},
{
"name": "Proteomics Standards Initiative Mass Spectrometry Ontology",
"uri": "https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo",
"version": "4.1.7"
}
]
and most importantly information about the metric values computed for a particular run.
"runQualities": [
{
...
}
]
In fact, runQualities can contain runQuality objects for multiple runs.
A different object setQualities may hold the QC information for groups of runs (shown in a different example).
A runQuality contains metadata (about the run, input files, the software used) and the computed qualityMetric objects.
{
"metadata": {
"inputFiles":
...
},
"qualityMetrics": [
...
]
}
The inputFiles consist of a single object, describing the source file with structured information about the file's name, format, location and other properties, defined via cv terms.
"inputFiles": [
{
"location": "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/09/PXD000966/CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.raw",
"name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.trfr.t3.mzML",
"fileFormat": {
"accession": "MS:1000584",
"name": "mzML format"
},
"fileProperties": [
{
"accession": "MS:1000747",
"name": "completion time",
"value": "2012-02-03 11:00:41"
},
{
"accession": "MS:1000569",
"name": "SHA-256",
"value": "82ff4545ab8ab85252a4c5bc2c62abbfd04021ef5fefce145386bf27ae663a0f"
},
{
"accession": "MS:1000031",
"name": "instrument model",
"value": "LTQ Orbitrap Velos"
}
]
As you can see, the location can not only be a filesystem location, but also a URL as you would get as part of a dataset submission to ProteomeXchange. Different metainformation can be included, too, like on which instrument model the run was acquired on, or the completion time of the mass spectrometry.
The example shows several simple metrics included in qualityMetrics, which are defined with their definition in the QC CV. The metrics provide quality information for the run with their values.
Metric values can be either single values,
"accession": "QC:4000059",
"name": "Number of MS1 spectra",
"value": 5074
tuple of values,
"accession": "QC:4000138",
"name": "MZ acquisition range",
"value": [ 300.157287597656,1778.8639 ]
or matrices or tables (shown in other examples).
{ "mzQC": {
"creationDate": "2020-12-01T11:56:34",
"version": "1.0.0",
"contactName": "Mathias Walzer",
"contactAddress": "walzer@ebi.ac.uk",
"runQualities": [
{
"metadata": {
"inputFiles": [
{
"location": "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/09/PXD000966/CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.raw",
"name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.trfr.t3.mzML",
"fileFormat": {
"accession": "MS:1000584",
"name": "mzML format"
},
"fileProperties": [
{
"accession": "MS:1000747",
"name": "completion time",
"value": "2012-02-03 11:00:41"
},
{
"accession": "MS:1000569",
"name": "SHA-256",
"value": "82ff4545ab8ab85252a4c5bc2c62abbfd04021ef5fefce145386bf27ae663a0f"
},
{
"accession": "MS:1000031",
"name": "instrument model",
"value": "LTQ Orbitrap Velos"
}
]
}
],
"analysisSoftware": [
{
"accession": "MS:1001058",
"name": "quality estimation by manual validation",
"version": "0",
"uri": "https://dx.doi.org/10.1021/pr201071t"
},
{
"accession": "QC:0000000",
"name": "QCCaclulator",
"version": "0.9.0",
"uri": "qccalculator.readthedocs.io"
}
]
},
"qualityMetrics": [
{
"accession": "QC:4000059",
"name": "Number of MS1 spectra",
"value": 5074
},
{
"accession": "QC:4000060",
"name": "Number of MS2 spectra",
"value": 14812
},
{
"accession": "QC:4000135",
"name": "Number of chromatograms",
"value": 1
},
{
"accession": "QC:4000138",
"name": "MZ acquisition range",
"value": [ 300.157287597656,1778.8639 ]
},
{
"accession": "QC:4000139",
"name": "RT acquisition range",
"value": [ 0.2959,5969.8172 ]
}
]
}
],
"controlledVocabularies": [
{
"name": "Proteomics Standards Initiative Quality Control Ontology",
"uri": "https://github.com/HUPO-PSI/qcML-development/blob/master/cv/v0_1_0/qc-cv.obo",
"version": "0.1.0"
},
{
"name": "Proteomics Standards Initiative Mass Spectrometry Ontology",
"uri": "https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo",
"version": "4.1.7"
}
]
}
}