Hi Eric,
Thanks for the explanation. The mzML and mzXML files are too big to upload to spctool-discuss. I uploaded the DP_Opti_Newpupi_15_2run_5May09.wiff and DP_Opti_Newpupi_15_2run_5May09.wiff.scan files. The mzML and mzXML files can be generated from the wiff file. I used the default options to generate mzML file and --mzXML option to generate mzXML file. Two mzML files was generated from the conversion, DP_Opti_Newpupi_15_2run_5May09-dp_2strun_newpupi_15.mzML and DP_Opti_Newpupi_15_2run_5May09-dp_2strun_newpupi_22.mzML. The one I said needs really long loading time is DP_Opti_Newpupi_15_2run_5May09-dp_2strun_newpupi_22.mzML. The loading time for DP_Opti_Newpupi_15_2run_5May09-dp_2strun_newpupi_15.mzML is short, but X!tandem report " No input spectra met the acceptance criteria". Two mzXML files also generated if I use -mzXML option. The search on DP_Opti_Newpupi_15_2run_5May09-dp_2strun_newpupi_22.mzXML doesn't produce any result, but the search on DP_Opti_Newpupi_15_2run_5May09-dp_2strun_newpupi_15.mzXML got about 1800 search hit. Thanks, Zhi -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Friday, October 02, 2009 9:33 PM To: [email protected] Cc: [email protected] Subject: [spctools-discuss] Re: msconvert generated mzML file And I believe there is one more clue missing from Jimmy's translation: when one of these WIFF files is converted to mzXML, then X!Tandem produces a good result. So item 1 is out, leaving just 2 or 3. Zhi, would you post a link to a zip file including a WIFF file, its mzML file, its mzXML file, and the respective search results from each file. Maybe some kind person would have a look at that zip file and see if the problem becomes apparent? Thanks, Eric > From: [email protected] [mailto:spctools- > > 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 > <[email protected]> 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 <[email protected] > >> <mailto:[email protected]>> wrote: > >> > >> > >> I just mean the mzML format itself. I used ReAdw to convert RAW > >> file to mzML > >> format. > >> > >> Thanks, > >> Zhi > >> > >> > >> -----Original Message----- > >> From: [email protected] > >> <mailto:[email protected]> > >> [mailto:[email protected] > >> <mailto:[email protected]>] On Behalf Of Matthew > >> Chambers > >> Sent: Friday, October 02, 2009 3:49 PM > >> To: [email protected] > >> <mailto:[email protected]> > >> 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 [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 -~----------~----~----~----~------~----~------~--~---
