findPeaks.MS1-methods: Collecting MS1 precursor peaks
In xcms: LC-MS and GC-MS Data Analysis

Description Arguments Details Value Methods Author(s) See Also

Collecting Tandem MS or MS$^n$ Mass Spectrometry precursor peaks as annotated in XML raw file

object

xcmsRaw object

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:

mzData: <spectrum id="463"> <spectrumInstrument msLevel="2"> <cvParam cvLabel="psi" accession="PSI:1000039" name="TimeInSeconds" value="92.7743"/> </spectrumInstrument> <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"/> </precursor> </spectrum>

mzXML: <scan num="17" msLevel="2" retentionTime="PT1.5224S"> <precursorMz precursorIntensity="125245">220.1828003</precursorMz> </scan>

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:

`mz, mzmin, mzmax`	annotated MS1 precursor selection mass
`rt, rtmin, rtmax`	annotated MS1 precursor retention time
`into, maxo, sn`	annotated MS1 precursor intensity