Precursor Intensity has a value of 0??

[rmflight]

When I read in the file using the xcms R package, the msnPrecursorIntensity has a value of 0. When comparing my two mzML files, I see these differences in the precursorList:

msconvert

<selectedIonList count="1">
            <selectedIon>
              <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="734.569152832031" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
              <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
              <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="1.7700104e07" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
</selectedIon>

ThermoRawFileParser

<selectedIonList count="1">
            <selectedIon>
              <cvParam cvRef="MS" accession="MS:1000744" value="734.569152832031" name="selected ion m/z" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
              <cvParam cvRef="MS" accession="MS:1000041" value="1" name="charge state" />
            </selectedIon>
</selectedIonList>

So it looks like the peak intensity for the selectedIon is missing from the ThermoRawFileParser.

Now, I don't do anything with MS2 scans in my work, and I'm processing my data in a very particular way, so I'm not sure how important this difference actually is, and whether any other software will care, but it is a difference I see, so I thought I should point it out.

These are both profile data conversions, btw. But I still don't see a value for the peak intensity if I generate centroided data either.

v117_snapshot

[nielshulstaert]

Hi @rmflight indeed the precursor intensity isn't there yet, neither in the MGF nor the mzML output. I've figured out how to calculate it for both centroid and profile data but I still need to test it. Also it will slow the conversion down so I might add it as (yet another) flag in a future release. It's also not clear to me whether this value is used by search engines for example.

[timosachsenberg]

I use the precursor intensity in one of my tools but have to admit that it usually doesn't help too much in improving results.

[hbarsnes]

@nielshulstaert Any update on getting the precursor intensity included in the mgf and mzml outputs?

[hbarsnes]

Please see #78 for an update on this issue.

[caetera]

Precursor intensity has been added in version 1.4.0, thus, I will close the issue.