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 -~----------~----~----~----~------~----~------~--~---
