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 <z...@systemsbiology.org > <mailto:z...@systemsbiology.org>> wrote: > > > Yes. I did. > > Zhi > > -----Original Message----- > From: 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: Monday, October 05, 2009 10:11 AM > To: spctools-discuss@googlegroups.com > <mailto: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-discuss@googlegroups.com> > > [mailto:spctools-discuss@googlegroups.com > <mailto:spctools-discuss@googlegroups.com>] On Behalf Of Matthew > Chambers > > Sent: Monday, October 05, 2009 9:56 AM > > To: spctools-discuss@googlegroups.com > <mailto: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-discuss@googlegroups.com> > >> [mailto:spctools-discuss@googlegroups.com > <mailto:spctools-discuss@googlegroups.com>] *On Behalf Of *Brian Pratt > >> *Sent:* Monday, October 05, 2009 9:41 AM > >> *To:* spctools-discuss@googlegroups.com > <mailto: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> > >> <mailto: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>> > >> [mailto: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> > >> <mailto: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> > >> <mailto: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> > >> <mailto: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>> > >> > >>>> <mailto: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>>> > >> > >>>> [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 > <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>> > >> > >>>> <mailto: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 -~----------~----~----~----~------~----~------~--~---
