Do you mean mzXML2Search instead of Mascot2XML? I agree that spectrum averaging should be a more universal feature; it's something I plan to put in msconvert but haven't gotten around to yet. What range of settings did you try for spectrum averaging in mzWiff?
-Matt Bill Nelson wrote: > We were never able to switch one of our labs over to TPP because they > use ABI Q-TOF with Mascot and the Mascot daemon produced an MGF file > that searched much better that the MGF file produced by mzWiff & > Mascot2XML. Through postings on this forum we learned that the better > performance (about 20% more hits) was due to the spectrum averaging > algorithm used by the daemon. There are settable arguments available > in the mzWiff program for spectrum averaging but they don't seem to do > anything in our hands. Plus, in my opinion, the averaging should be > performed in the Mascot2XML program, leaving the mzXML to reflect the > original raw data. > Has anybody had any experience in addressing this issue with wiff to > mgf? > > Thanks, > Bill > > On Feb 16, 1:13 pm, Matthew Chambers <[email protected]> > wrote: > >> It depends what you want to use the MGF for. I think the TPP pipeline >> for the near future should continue using mxXML2Search for MGF output >> because of the way Mascot2XML expects the TITLE line to be formatted. In >> a future msconvert version, scan-number-only files like mzXML or Thermo >> RAW should convert to the DTA-style TITLE format that TPP is used to >> (except I don't think it does the 0-padding). On the other hand, if you >> don't care about using the MGF or its downstream products in the TPP, >> msconvert is easy to use for this purpose. >> >> -Matt >> >> Brian Pratt wrote: >> >>> The msconvert tool should handle that: >>> >>> To convert foo.mzxml to foo.mgf >>> >>> msconvert --mgf foo.mzxml >>> >>> -----Original Message----- >>> From: [email protected] >>> [mailto:[email protected]] On Behalf Of Bright >>> Sent: Monday, February 16, 2009 6:20 AM >>> To: spctools-discuss >>> Subject: [spctools-discuss] How to convert mzXML file to mgf file >>> >>> Hi everyone >>> I can't deal with the problem that convert mzXML file to mgf file. >>> Could your give me some ideal to over it. >>> Thank. >>> --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
