Hi Brian, Hi Jimmy,
Thanks to both of you for your answers. Actually Jimmy was right: the precursor was falling off the high mass cut-off. Note that the -T option is not documented in the MzXML2Search options (just when you run the "MzXML2Search" command to see the possible options). Might be interesting to list it there too, for other people that may encounter the same issues as I did. But anyway thanks again for your quick reply and to have solved my issues :) Best, Ludovic On Nov 24, 8:04 am, Jimmy Eng <[email protected]> wrote: > 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 > > athttp://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.
