Hi, I'm working with MRM data and I would analize them using xcms. I have encountered some trouble and I'm not still able to read the data using xcms. I've searched into the forum to try to understand if xcms is able to work with MRM data or not but, I haven't found any recent discussion about that...
This is what I've done:
1 - MRM data aquired with AB-Sciex QQQ
2 - wiff file converted using msConvert (ProteoWizard) into mzML.
Now when I try to run xcmsRaw I obtain this:
[SpectrumList_mzML::spectrum()] Index out of bounds.
Seems that no spectral information are contained into the mzML file but, if I try to open it using seeMS from proteo wizard I see all my MRM experiment...
Have you ever experienced a problem like this??
All the best
I have never tried it myself but have you tried playing with the includeMSn and mslevel parameters in xcmsRaw? My guess would be that includeMSn=TRUE might do the trick.
Opening your mzML file in a text editor might also give you an idea how the data has been written.
Now I also have MRM data from AB-Sciex QQQ... Neither mzMine nor XCMS can read the file generated by msconvert, but seeMS shows the data as Ricca said. I do get another error from XCMS though:
Any ideas of how to read this data?
Each scan looks like this:
<chromatogram index="1" id="SRM SIC Q1=86.01 Q3=69 sample=1 period=1 experiment=1 transition=0" defaultArrayLength="380">
<cvParam cvRef="MS" accession="MS:1001473" name="selected reaction monitoring chromatogram" value=""/>
<userParam name="MS_dwell_time" value="0.029999999999999999" type="xs:float"/>
<precursor>
<isolationWindow>
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="86.01" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
</isolationWindow>
<activation>
<cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="0.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
<userParam name="MS_declustering_potential" value="0" type="xs:float"/>
</activation>
</precursor>
<product>
<isolationWindow>
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="69.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
</isolationWindow>
</product>
<binaryDataArrayList count="2">
<binaryDataArray encodedLength="3236"><cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
<cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
<cvParam cvRef="MS" accession="MS:1000595" name="time array" value="" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<binary>..............................</binary>
</binaryDataArray><binaryDataArray encodedLength="1156">
<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
<cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
<binary>......
</binary>
</binaryDataArray>
</binaryDataArrayList>
...
...
</chromatogram>
Hi,
there are several ways how MRM can be encoded in the mzML,
1) as "degraded" MS2 spectra with single-point spectra (==intensity of the product ion)
2) as <chromatogram>, which was one of the extensions of mzML over mzXML/mzData.
pwiz has for some vendors an "--srmAsSpectra : write selected reaction monitoring as spectra,
not chromatograms" option (http://proteowizard.sourceforge.net/too ... nvert.html (http://proteowizard.sourceforge.net/tools/msconvert.html))
So 1) might work if you msn2xcmsRaw() the data beforehand.
XCMS currently can't handle <chromatogram>s, but since last your it should
have become easier to extract them from mzR using the new pwiz backend.
Yours,
Steffen
Hi,
I tried --simAsSpectra and --srmAsSpectra now but I get identical files. So I guess AB-Sciex doesn't support it...
I was exactly thinking/hoping I could read them as MSn data.