Ludovic, Given that you're looking for 5+/6+ peptides, can you check to make sure the peptide masses are not above the high mass cutoff default (4200 Da) for MzXML2Search? If so, you would use the -T option to specify a higher mass cutoff e.g. MzXML2Search -mgf -T8000.0 file.mzXML
- Jimmy On Sun, Nov 22, 2009 at 11:50 PM, lgillet <[email protected]> wrote: > 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=. > > > -- 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=en.
