Collecting Tandem MS or MS$^n$ Mass Spectrometry precursor peaks as annotated in XML raw file
Some mass spectrometers can acquire MS1 and MS2 (or MS$^n$ scans) quasi simultaneously, e.g. in data dependent tandem MS or DDIT mode.
Since xcmsFragments attaches all MS$^n$ peaks to MS1 peaks in xcmsSet, it is important that findPeaks and xcmsSet do not miss any MS1 precursor peak.
To be sure that all MS1 precursor peaks are in an xcmsSet, findPeaks.MS1 does not do an actual peak picking, but simply uses the annotation stored in mzXML, mzData or mzML raw files.
This relies on the following XML tags:
<cvParam cvLabel="psi" accession="PSI:1000039" name="TimeInSeconds" value="92.7743"/>
<precursor msLevel="1" spectrumRef="461">
<cvParam cvLabel="psi" accession="PSI:1000040" name="MassToChargeRatio" value="462.091"/>
<cvParam cvLabel="psi" accession="PSI:1000042" name="Intensity" value="366.674"/>
<scan num="17" msLevel="2" retentionTime="PT1.5224S">
Several mzXML and mzData converters are known to create incomplete files, either without intensities (they will be set to 0) or without the precursor retention time (then a reasonably close rt will be chosen. NYI).
A matrix with columns:
annotated MS1 precursor selection mass
annotated MS1 precursor retention time
annotated MS1 precursor intensity
Steffen Neumann, [email protected]
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