Get MS3 spectrum parent scan index

[wenbostar]

I have an mzML file that contains both MS2 and MS3 spectra. I used the following code to extract MS3 spectra data. For each MS3 spectrum, I want to extract the scan number of its parent MS2 spectrum. This information can be found in the section of "precursorList" of the MS3 spectrum. Which function should I use?

MZMLFile source = new MZMLFile("test.mzML");
LCMSRunInfo lcmsRunInfo = null;
try {
    lcmsRunInfo = source.fetchRunInfo();
} catch (FileParsingException e) {
    e.printStackTrace();
}
source.setNumThreadsForParsing(cores);
MZMLIndex mzMLindex = null;
try {
    mzMLindex = source.fetchIndex();
} catch (FileParsingException e) {
    e.printStackTrace();
}

IScanCollection scans;
scans = new ScanCollectionDefault(true);
scans.setDataSource(source);
scans.loadData(LCMSDataSubset.WHOLE_RUN, StorageStrategy.STRONG);

TreeMap<Integer, IScan> num2scanMap = scans.getMapNum2scan();
Set<Map.Entry<Integer, IScan>> num2scanEntries = num2scanMap.entrySet();

int total_spectra = 0;

for (Map.Entry<Integer, IScan> next : num2scanEntries) {
    IScan scan = next.getValue();
    if (scan.getSpectrum() != null) {
        if (scan.getMsLevel() == 3) {
            // extract the scan number of the MS2 spectrum that this MS3 spectra derived from.
        }
    }
}

Here is an example raw file that contains both MS2 and MS3 spectra: https://www.ebi.ac.uk/pride/data/archive/2019/07/PXD010557/PT6374-1.raw.

[chhh]

The scan IDs in mzML are actually free-text, this is not a standard, and you can even change the way IDs are generated when converting to mzML with ProteoWizard. So I woudn't recommend trying to parse it directly as these things change over time and will vary depending on the version of msconvert used to perform the conversion.

Also, it is not guaranteed that those "parent" scans are even in the mzML file anymore, some people do the conversion and cut out all MS1 scans, for example.

That being said, there are 2 methods in PrecursorInfo class:

• getParentScanRefRaw() returns the whole spectrumRef string that you've shown in the screenshot.
• getParentScanNum() returns the scan number that MSFTBX tried to infer from the spectrum ref.

IScan ms3scan = scans.getMapMsLevel2index().get(3).getNum2scan().get(0);
PrecursorInfo precursor = ms3scan.getPrecursor();
String parentScanRefRaw = precursor.getParentScanRefRaw();
Integer parentScanNum = precursor.getParentScanNum();

[wenbostar]

Thank you so much for your detailed explanation. It's very helpful.