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