My mistake: I think I was too tired and I skipped that line. Sorry for that and many thanks again for the tip and the solution to my problems! Best, Ludovic
On Nov 24, 6:26 pm, Brian Pratt <[email protected]> wrote: > FWIW, the -T option actually does get a mention in the usage statement, > " -T<num> where num is a float specifying maximum MH+ scan, > default=4200.0 Da" > although it refers to "maximum scan" instead of "maxmum mass", which may > have caused your eye to trip over it. I'll fix that. Thanks for the > pointer. > > Brian > > On Tue, Nov 24, 2009 at 8:16 AM, lgillet <[email protected]> wrote: > > 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]<spctools-discuss%[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]<spctools-discuss%[email protected]> > > . > > For more options, visit this group at > >http://groups.google.com/group/spctools-discuss?hl=en. -- 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.
