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