Hi, I am running into trouble during the MzXML2Search export from mzXML to mgf.
Here is what I observe: - if you simply run "MzXML2Search -mgf file.mzXML", some scans do not get properly exported. I did not yet figure out the "rule" behind this behavior, but this was particularly obvious to me since I was expecting a set of specific 5+ or 6+ peptides. I checked in the mzXML file and the expected precursor masses are indeed there, and with the correct charge state properly assigned by the mass spec instrument (QTOF). But those MS2 scans corresponding to the precursors are clearly absent from the mgf. - I found a message from another user in this list suggesting the possibility to export specific charge states. So I run the command "MzXML2Search -mgf -C2-6 file.mzXML", and while the first scans get properly exported (you get the 2+, 3+, 4+, 5+, 6+ reports for each MS2 scan), the specific precursor I am looking for (scan=2643) gets exported only as charge 1+, 2+, 3+, 4+?!?!? Have somebody reported this before? Is there any option that I am not aware of that could fix this issue? I am happy to provide the mzXML file and specific example of set of peptides that are not properly handled during the MzXML2Search export, so that you may troubleshoot those by yourself. Thanks in advance for your help with this. I really hope that will help also other people too. Best, Ludovic -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=.
