Returning to the behavior of mzXML2Search, just eyeballing the code I don't see any reason it should fail at scan numbers > 99999. Perhaps the problem is actually downstream from mzXML2Search? While mzXML2Search should quite happily emit 6 digit MGF scan numbers, I can imagine a consumer of MGF might not see that coming.
Perhaps you could furnish an example of the msconvert output that's giving you trouble? Eyeballing the code only gets one so far, it's ideal to see it actually running in the debugger. Brian Pratt On Tue, Nov 17, 2009 at 6:33 AM, Dave Trudgian <[email protected]> wrote: > > Matt, > > We just apply a (low) absolute threshold. Different values for different > instruments, but it's most critical on the Agilent and Water's QTOFs, as > without any threshold there are 1000s of peaks. > > Look forward to seeing the filtering in msconvert. > > DT > > > Matt Chambers wrote: > > What kind of thresholding do you do? Enabling that in msconvert is > > overdue - the backend code to support it is already in place. > > > > MzXML2Search is failing because it depends on a strict DTA name scheme > > with 5 digits. This is going to break with long LTQ Velos runs so it > > needs to be fixed regardless of the Agilent scanId issue. It's ironic > > that a Thermo file is the one to break the Thermo-centric assumptions. :P > > > > -Matt > > > > > > dctrud wrote: > >> MzXML2Search conversion to mgf fails for me on mzXML / mzML created > >> using msconvert from Agilent 6520 QTOF data. > >> > >> Trapper numbers spectra using an index starting at 1, whilst msconvert > >> uses the Agilent scan ID (can be a very large number). MzXML2Search > >> conversion of the resulting file into mgf then fails once it reaches a > >> scan ID > 99,999. > >> > >> Have seen similar problems with other programs and contacted Matt > >> Chambers who said that the numbering would stay the same, and that > >> it's better if programs which can't cope with the large numbers are > >> fixed. Is this possible (desirable?) for MzXML2Search and any other > >> TPP tools that might be affected? > >> > >> I can't use Trapper as I need to extract Profile MS + Centroid MS/MS > >> from a dual mode file (msconvert supported). I can't directly convert > >> to mgf with msconvert as I need to do peak thresholding to get file > >> sizes down to a reasonable level. > >> > >> Cheers, > >> > >> DT > > > > > > > > > > -- > Dr. David Trudgian > Bioinformatician in Proteomics > University of Oxford > > Mon-Thu: CCMP, Roosevelt Drive > Tel: (+44) (01865 2)87784 > > Friday : Dunn School of Pathology, S. Parks Rd. > Tel: (+44) (01865 2)75557 > > > > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
