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