Hi Matt, Msconvert looks to be producing .mzXML 2.0 by default. This is causing an issue for the downstream software (Progenesis LC-MS). Does msconvert support any later versions of .mzXML?
Thanks, Ben On Sep 30, 4:46 pm, Ben Collins <[email protected]> wrote: > Hi Moshe, > > I'm currently using Progenesis LC-MS, a commercial label free analysis > software. The feature finding takes a long time. I have also been able to > analyse some of this data with msInspect. > > Cheers, > Ben > > On Fri, Sep 25, 2009 at 7:34 AM, Moshe Olshansky <[email protected]>wrote: > > > > > Hi Ben, > > > Just out of curiosity, what tools can handle your "small" 14 GB file? > > > Regards, > > > Moshe. > > > > Hi Matt, > > > > Thanks, this seems to have done the trick. I now have a 14 GB mzXML file > > > instead of 50 GB. > > > > I am interested to know whether the peak picking is being done with > > > MassHunter or Proteowizard in this case? > > > > Many thanks, > > > Ben. > > > > On Thu, Sep 24, 2009 at 2:21 PM, Matt Chambers < > > > [email protected]> wrote: > > > >> Hi Ben, > > > >> 50gb for one file? That's impressive. That could be much improved with > > >> compression (which the Agilent MH format also does), but since you need > > >> to peak pick the MSn to identify them in most search engines, try this > > >> command: > > >> msconvert source.d --mzXML --filter "peakPicking true [2,2]" > > >> There is a bug in msconvert's Reader_Agilent (actually I think it's in > > >> MHDAC; I'm looking into it now with Agilent) that sometimes will always > > >> centroid profile data no matter whether it was requested or not. So even > > >> though the above command doesn't specify to peak pick the MS1s, it may > > >> do so anyway. If that's the case, let me know and I can get you a fixed > > >> build with a workaround in place. > > > >> -Matt > > > >> Ben Collins wrote: > > >> > Hi all, > > > >> > I have data from an Agilent QTOF (.d) collected in profile mode (both > > >> > MS1 and MS2) and I would like to convert to mzXML which I can do with > > >> > Trapper or msconvert. The question I have is, is it possible to > > >> > perform centroiding only on the MS2 data while leaving the MS1 data in > > >> > profile mode? > > > >> > Unfortunately it's not currently possible to collect MS1 in profile > > >> > and MS2 in centroid on this instrument (I have requrested it from the > > >> > vendor). The issue is that if both files are in profile mode the files > > >> > is pretty unmanageable (up to 50 GB) but I need to keep the MS1 data > > >> > in profile to do AMT/label free analysis. > > > >> > Thanks, > > >> > Ben --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
