Hi, thanks a lot for developing TPP, it's a great set of tools.
I'm trying to analyze DDA data (Top 5 method) from a Waters Xevo QTOF but there seems to be a problem with identifying MSMS spectra in the mzml files generated from the .raw folders through MSconvert, which is likely caused by multiple MSMS spectra stored in different "functions" having the same spectra index. The Comet or X!tandem search completes without errors but the spectra number being searched is only about half of all MSMS spectra in the file and the spectra linked in the pep.xml don't fit with the identifications (in terms of matching fragments and precursor mass). When I process the raw data in PLGS and export as MGF, followed by conversion to mzml in MSconvert, the scans get a function-independent consecutive index and the search results seem to be correct. While this is fine for peptide identification, PLGS doesn't allow me to export the MS1 spectra that I need for the down-stream quantification. So it's not a viable alternative. Can TPP handle a two dimensional spectra index (Function=x Spectrum=y)? Or can I set MSconvert to generate a one-dimensional index that preserves the association between MS1 and MS2 spectra of each DDA cycle? I ran MSconvert with the "write index" option but that doesn't seem to generate such an index. Thank you for your help, David Schmidt -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/ad4e2c4d-787b-48ff-aa1b-8ea78227f6d9%40googlegroups.com.
