I'll be a translator. Zhi seems to be having issues with ABI QQQ wiff files. They were translated to mzML using msconvert and X!Tandem didn't like them. She mentioned ReAdW only to state that X!Tandem was able to process some unrelated mzML files in the past.
The problem could be: 1) the QQQ file really has no good ms/ms spectra in it. 2) there's a problem with the QQQ to mzML conversion. 3) everything's fine with the data but for whatever reason X!Tandem can't handle the particular mzML correctly. 4) the X!Tandem spectral processing parameters are set weird. Even money on the first 3. On Fri, Oct 2, 2009 at 4:31 PM, Matthew Chambers <matthew.chamb...@vanderbilt.edu> wrote: > > I'm lost. You said "recently I used the msconvert to convert some QQQ > wiff files to mzML format". Are we talking about ABI WIFF or Thermo RAW? > > -Matt > > > Brian Pratt wrote: >> You probably mean mzXML rather than mzML? >> >> On Fri, Oct 2, 2009 at 3:55 PM, Zhi Sun <z...@systemsbiology.org >> <mailto:z...@systemsbiology.org>> wrote: >> >> >> I just mean the mzML format itself. I used ReAdw to convert RAW >> file to mzML >> format. >> >> Thanks, >> Zhi >> >> >> -----Original Message----- >> From: spctools-discuss@googlegroups.com >> <mailto:spctools-discuss@googlegroups.com> >> [mailto:spctools-discuss@googlegroups.com >> <mailto:spctools-discuss@googlegroups.com>] On Behalf Of Matthew >> Chambers >> Sent: Friday, October 02, 2009 3:49 PM >> To: spctools-discuss@googlegroups.com >> <mailto:spctools-discuss@googlegroups.com> >> Subject: [spctools-discuss] Re: msconvert generated mzML file >> >> >> Hi Zhi, >> >> You say it worked fine with ReAdW; do you mean mzWiff? If so, what >> conversion settings did you use (for both msconvert and mzwiff)? >> >> -Matt >> >> >> Zhi Sun wrote: >> > Hi All, >> > >> > Recently I used the msconvert to convert some QQQ wiff files to mzML >> format, >> > and did X!tandem search using those mzML files. I ran into a >> problem. >> > X!tandem took really long time (2 or more hours) for loading the >> spectra, >> > and them after it finally finished loading, it just reported >> "Loaded, No >> > input spectra met the acceptance criteria." The X!tandem runs >> fine on >> other >> > mzML file. I tested on one mzML which was generated by ReAdw before. >> > >> > When doing the conversion, I used default options for msconvert. >> Does >> anyone >> > of you know what could be the reason for this? If necessary, I >> could send >> > the wiff file and also the mzML file. >> > >> > Thanks, >> > Zhi >> > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
