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 <z...@systemsbiology.org> wrote: > > Yes. I did. > > Zhi > > -----Original Message----- > From: spctools-discuss@googlegroups.com > [mailto:spctools-disc...@googlegroups.com] On Behalf Of Matthew Chambers > Sent: Monday, October 05, 2009 10:11 AM > To: spctools-discuss@googlegroups.com > 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: spctools-discuss@googlegroups.com > > [mailto:spctools-disc...@googlegroups.com] On Behalf Of Matthew Chambers > > Sent: Monday, October 05, 2009 9:56 AM > > To: spctools-discuss@googlegroups.com > > 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:* spctools-discuss@googlegroups.com > >> [mailto:spctools-disc...@googlegroups.com] *On Behalf Of *Brian Pratt > >> *Sent:* Monday, October 05, 2009 9:41 AM > >> *To:* spctools-discuss@googlegroups.com > >> *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 <z...@systemsbiology.org > >> <mailto:z...@systemsbiology.org>> 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:* spctools-discuss@googlegroups.com > >> <mailto:spctools-discuss@googlegroups.com> > >> [mailto:spctools-discuss@googlegroups.com > >> <mailto:spctools-discuss@googlegroups.com>] *On Behalf Of *Brian Pratt > >> *Sent:* Monday, October 05, 2009 9:20 AM > >> > >> > >> *To:* spctools-discuss@googlegroups.com > >> <mailto:spctools-discuss@googlegroups.com> > >> > >> *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 <jke...@gmail.com > >> <mailto:jke...@gmail.com>> 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 > >> <matthew.chamb...@vanderbilt.edu > >> <mailto:matthew.chamb...@vanderbilt.edu>> 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 <z...@systemsbiology.org > >>>> > >> <mailto:z...@systemsbiology.org> > >> > >>>> <mailto:z...@systemsbiology.org <mailto:z...@systemsbiology.org>>> > >>>> > >> wrote: > >> > >>>> I just mean the mzML format itself. I used ReAdw to convert RAW > >>>> file to mzML > >>>> format. > >>>> > >>>> Thanks, > >>>> Zhi > >>>> > >>>> > >>>> -----Original Message----- > >>>> From: spctools-discuss@googlegroups.com > >>>> > >> <mailto:spctools-discuss@googlegroups.com> > >> > >>>> <mailto:spctools-discuss@googlegroups.com > >>>> > >> <mailto:spctools-discuss@googlegroups.com>> > >> > >>>> [mailto:spctools-discuss@googlegroups.com > >>>> > >> <mailto:spctools-discuss@googlegroups.com> > >> > >>>> <mailto:spctools-discuss@googlegroups.com > >>>> > >> <mailto:spctools-discuss@googlegroups.com>>] On Behalf Of Matthew > >> > >>>> Chambers > >>>> Sent: Friday, October 02, 2009 3:49 PM > >>>> To: spctools-discuss@googlegroups.com > >>>> > >> <mailto:spctools-discuss@googlegroups.com> > >> > >>>> <mailto:spctools-discuss@googlegroups.com > >>>> > >> <mailto:spctools-discuss@googlegroups.com>> > >> > >>>> 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 spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
