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 -~----------~----~----~----~------~----~------~--~---
