Well that is definitely a bug in Tandem's reader, because there are no spectra in the smaller file, just chromatograms. You can safely exclude it.
-Matt Zhi Sun wrote: > Hi Matt, > > Actually the tandem took longer time on loading the smaller mzML file, which > is only 331k. I think this is a MIDAS run. > > Zhi > > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Matthew Chambers > Sent: Monday, October 05, 2009 12:40 PM > To: [email protected] > Subject: [spctools-discuss] Re: msconvert generated mzML file > > > OK. It worked as expected. Your spectra look like I'd expect QQQ full > spectra to look: messy... oops, I mean a signal-rich. :) Tandem really > took 30+ minutes to load that 20mb file? That might have more to do with > Brian's observation that Insilicos Viewer couldn't read it. I can't see > why it would be problematic looking at the file though. Maybe the > presence of chromatograms? Zhi, is this a MIDAS run? > > -Matt > > > Zhi Sun wrote: > >> It is there now. >> >> Thanks, >> Zhi >> >> -----Original Message----- >> From: [email protected] >> [mailto:[email protected]] On Behalf Of Matthew Chambers >> Sent: Monday, October 05, 2009 11:48 AM >> To: [email protected] >> Subject: [spctools-discuss] Re: msconvert generated mzML file >> >> >> It does load in SeeMS, and it is profile mode data. >> >> Zhi, is the mzML on peptideAtlas the result after you added the >> peakPicking filter? >> >> -Matt >> >> >> Brian Pratt wrote: >> >> >>> FWIW those mzML files don't load in InsilicosViewer, which uses the >>> same pwiz libs as tandem for reading. I'm investigating. The mzXML >>> files load fine, though. >>> >>> On Mon, Oct 5, 2009 at 10:36 AM, Zhi Sun <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> >>> Yes. I did. >>> >>> Zhi >>> >>> -----Original Message----- >>> From: [email protected] >>> <mailto:[email protected]> >>> [mailto:[email protected] >>> <mailto:[email protected]>] On Behalf Of Matthew >>> Chambers >>> Sent: Monday, October 05, 2009 10:11 AM >>> To: [email protected] >>> <mailto:[email protected]> >>> Subject: [spctools-discuss] Re: msconvert generated mzML file >>> >>> >>> Yeah, that sounds bad, you can kill that because it's almost >>> > certainly > >>> still profile data. Did you use the exact syntax I gave for the >>> > filter > >>> parameter? >>> --filter "peakPicking true [1,2]" >>> >>> Just "peakPicking true [1,2]" is not enough. >>> >>> -Matt >>> >>> >>> Zhi Sun wrote: >>> > Hi Matt, >>> > >>> > I know it hasn't passed 2 hour :), but 30mins has passed, and it >>> is still >>> > loading the spectra. I just took a guess that the problem is >>> stills there. >>> >>> > >>> > Zhi >>> > >>> > -----Original Message----- >>> > From: [email protected] >>> <mailto:[email protected]> >>> > [mailto:[email protected] >>> <mailto:[email protected]>] On Behalf Of Matthew >>> Chambers >>> > Sent: Monday, October 05, 2009 9:56 AM >>> > To: [email protected] >>> <mailto:[email protected]> >>> > Subject: [spctools-discuss] Re: msconvert generated mzML file >>> > >>> > >>> > It's impossible you had the same error you reported before: >>> > >>> > >>> >> I ran into a problem. X!tandem took really long time (2 or >>> more hours) >>> >> >>> > for loading the spectra, >>> > >>> > Since it hasn't been two hours, I know it must be a new error. Or >>> > at > >>> > least, it must have gotten to the error much faster. :) >>> > >>> > Presumably the file is now much smaller? >>> > >>> > -Matt >>> > >>> > >>> > Zhi Sun 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]> >>> >> [mailto:[email protected] >>> <mailto:[email protected]>] *On Behalf Of *Brian >>> > Pratt > >>> >> *Sent:* Monday, October 05, 2009 9:41 AM >>> >> *To:* [email protected] >>> <mailto:[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] <mailto:[email protected]> >>> >> <mailto:[email protected] >>> <mailto:[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]> >>> >> <mailto:[email protected] >>> <mailto:[email protected]>> >>> >> [mailto:[email protected] >>> <mailto:[email protected]> >>> >> <mailto:[email protected] >>> <mailto:[email protected]>>] *On Behalf Of *Brian >>> Pratt >>> >> *Sent:* Monday, October 05, 2009 9:20 AM >>> >> >>> >> >>> >> *To:* [email protected] >>> <mailto:[email protected]> >>> >> <mailto:[email protected] >>> <mailto:[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] >>> <mailto:[email protected]> >>> >> <mailto:[email protected] <mailto:[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] >>> <mailto:[email protected]> >>> >> <mailto:[email protected] >>> <mailto:[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]> >>> >>>> >>> >> <mailto:[email protected] <mailto:[email protected]>> >>> >> >>> >>>> <mailto:[email protected] >>> <mailto:[email protected]> <mailto:[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]>> >>> >> >>> >>>> <mailto:[email protected] >>> <mailto:[email protected]> >>> >>>> >>> >> <mailto:[email protected] >>> <mailto:[email protected]>>> >>> >> >>> >>>> [mailto:[email protected] >>> <mailto:[email protected]> >>> >>>> >>> >> <mailto:[email protected] >>> <mailto:[email protected]>> >>> >> >>> >>>> <mailto:[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]> >>> >>>> >>> >> <mailto:[email protected] >>> <mailto:[email protected]>> >>> >> >>> >>>> <mailto:[email protected] >>> <mailto:[email protected]> >>> >>>> >>> >> <mailto:[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 -~----------~----~----~----~------~----~------~--~---
