That also at least partly explains why InsilicosViewer doesn't read it, then.
Well, that and (in my case) WinZip helpfully expanding LF to CRLF, and RAMPAdapter tipping over when the index didn't line up as a result. It would be nice if it would just ignore the index at that point instead of throwing an exception. Brian On Mon, Oct 5, 2009 at 12:59 PM, Matthew Chambers < [email protected]> wrote: > > 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 -~----------~----~----~----~------~----~------~--~---
