Zhi, Did you use this option? --filter "peakPicking true [1,2]"
-Matt Zhi Sun wrote: > > 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 -~----------~----~----~----~------~----~------~--~---
