Does the WIFF file contain the profile data? If it does, then that's what msconvert will retrieve by default. So if it does, try msconvert's output again with that filter enabled.
-Matt Zhi Sun wrote: > No. I didn't use that. > > Zhi > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Matthew Chambers > Sent: Monday, October 05, 2009 9:05 AM > To: [email protected] > Subject: [spctools-discuss] Re: msconvert generated mzML file > > > 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. > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
