Example of mzQC metrics in mzML
QC metrics from mzQC can also be incorporated into other PSI formats, like mzML and mzIdentML, if it is preferable to keep all information in one file.
The following describes a tiny mzML, for which a QC tool calculated id-free QC metrics for all individual spectra of the run and a set of charge distribution metrics.
Due to the shared design properties of mzQC, metrics can be directly represented as XML <cvParam> elements, however their location bound to mzML schema constraints.
The first addition to the mzML is the source from which the metrics came from, for reference to more QC information on the run and documentation.
<sourceFile id="QC1" name="BSA1_F1.mzQC" location="file:///examples/">
<cvParam cvRef="MS" accession="MS:1003160" name="mzQC format" />
</sourceFile>
Next, the metrics computed for the whole run can be be deposited as a child of the <run> element itself. Metric objects from mzQC can be directly translated into <cvParam> elements.
<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" startTimeStamp="2009-08-09T22:32:31" defaultSourceFileRef="sf_ru_0">
<cvParam cvRef="MS" accession="MS:4000063" name="MS2 known precursor charges fractions" value="{'MS:1000041': [1,2,3,4], 'UO:0000191': [0,0.5721,0.3535,0.0743]}" />
<userParam name="mzml_id" type="xsd:string" value="20090810_SvNa_QC_BSA50fmol.RAW"/>
Please note that for example brevity purposes the mzML was truncated to 3 spectra, however the metrics were calculated on the whole to reflect realistic values. Also, the NativeID format was truncated to the index of spectrum= bit.
Next, the spectra metrics can be put as children of <spectrum> elements, in the same fashion as for the run metrics.
<spectrumList count="3" defaultDataProcessingRef="dp_sp_0">
<spectrum id="spectrum=1011" index="0" defaultArrayLength="467" dataProcessingRef="dp_sp_0">
<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
<cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="391.284088134766023"/>
<cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="9.2884425e05"/>
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="6.937649e06"/>
<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.000828877017"/>
<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2008.458458829989922"/>
<cvParam cvRef="MS" accession="MS:4000068" name="spectra half-TIC" value="{'MS:1000767': [1011], 'UO:0000191': [0.0235]}"/>
<userParam name="filter string" type="xsd:string" value="FTMS + p NSI Full ms [300.00-2000.00]"/>
<userParam name="preset scan configuration" type="xsd:string" value="1"/>
<scanList count="1">
<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
<scan >
<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="1501.41394042969" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
<scanWindowList count="1">
<scanWindow>
<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="300" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
</scanWindow>
</scanWindowList>
</scan>
</scanList>
<binaryDataArrayList count="2">
<binaryDataArray encodedLength="4984">
<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
<binary>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</binary>
</binaryDataArray>
<binaryDataArray encodedLength="2492">
<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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</spectrum>
<spectrum id="spectrum=1012" index="1" defaultArrayLength="478">
...
As you can seen in the <cvParam> elements, it contains extra information in cvRef.
This attribute is a reference to a data entry registering the controlled vocabularies used in the file much like in mzQC.
This has to be added to finalise the mzML.
The <cv> elements are again very similar to the respective entries in mzQC, making translation easy.
<cvList count="5">
<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>
<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>
<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
</cvList>
Note that you should also add your software to <software> and <dataProcessing>.