We'll chase this down. Note for anyone else looking at these files, there's a typo in one of the links on that page, actual links are http://www.peptideatlas.org/repository/tmp/DP_Opti_Newpupi_mzML.tar.gz http://www.peptideatlas.org/repository/tmp/DP_Opti_Newpupi_mzXML.tar.gz http://www.peptideatlas.org/repository/tmp/DP_Opti_Newpupi_wiff.tar.gz
Brian On Mon, Oct 5, 2009 at 9:52 AM, Zhi Sun <[email protected]> wrote: > Thanks Brian. I just tried using the "peakPicking true [1,2]" to convert > the file. It seems to produce the same error. > > > > Best, > > Zhi > > > ------------------------------ > > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *Brian Pratt > *Sent:* Monday, October 05, 2009 9:41 AM > > *To:* [email protected] > *Subject:* [spctools-discuss] Re: msconvert generated mzML file > > > > Well, I learned something today! Sounds worth avoiding, though - msconvert > is the coverter of choice moving forward. especially for mzML output. > > > > I'll have a quick look at the mzML and mzXML equivalent msconvert outputs > from the X!Tandem point of view, since I'm the one that added that to > X!Tandem. > > > > Brian > > On Mon, Oct 5, 2009 at 9:30 AM, Zhi Sun <[email protected]> wrote: > > Hi Brian, > > > > I have post the mzML, mzXML and also the wiff file to > http://www.peptideatlas.org/repository/tmp/ if anyone is interested in > taking a look. > > > > ReAdw have an option –mzML, it is “EXPERIMENTAL”. The version I used was > 4.3.0. I haven’t checked if there is a newer version out there. I have > checked with my colleague with the X!tandem version. He said the X!tandem > version we use should be same as the one in currently released TPP. > > > > Thanks, > > Zhi > ------------------------------ > > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *Brian Pratt > *Sent:* Monday, October 05, 2009 9:20 AM > > > *To:* [email protected] > > *Subject:* [spctools-discuss] Re: msconvert generated mzML file > > > > I don't think Readw ever made mzML files did it? Probably the user is > thinking of mzXML there. > > > > X!Tandem's mzML reader is from the same library as msconvert's writer > (assuming we're talking about the TPP build of X!Tandem), so a mismatch is > unlikely. > > > > I think the problem probably isn't within the tools themselves, in this > particular case, but in what data they're being fed. > > > > Brian > > On Fri, Oct 2, 2009 at 4:53 PM, Jimmy Eng <[email protected]> wrote: > > > 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 > >> > > > > > > > > > > > <br > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
