From: Matt C. <mat...@gm...> - 2011-05-30 15:42:27
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Hi Florian, Unfortunately neither the Waters API nor the new ABI API provides access to peak picking. So either you have to have centroided at acquisition (in instrument method) or you can try using pwiz's internal peak picking which is not yet very good. The 0 or 1 you see are just noise samples, the kind of things that would be eliminated by peak picking. -Matt On 5/30/2011 6:36 AM, Florian P. Breitwieser wrote: > Hi developers, > > thanks for providing ProteoWizard, we use msconvert already for > processing Orbitrap RAW files. > > I have a problem generating a MGF out of Waters/MassLynx .raw folders: > Peak picking seems not to work (even tough it is set) and MS2 intensity > is always 0 or 1. Note: MassLynx is not installed, do I need it? > > Example output MGF: > BEGIN IONS > TITLE=function=2 process=0 scan=1 > RTINSECONDS=1431.674994 > PEPMASS=732.3067626953125 > 99.04961395 0 > 99.05695343 1 > 99.06429291 0 > 101.9856644 0 > 101.9931259 1 > 102.0005875 0 > 114.0172958 0 > 114.0251846 1 > 114.0330734 0 > ... > > ProteoWizard release: 2.1.2736 (2011-5-29) > ProteoWizard MSData: 2.1.2735 (2011-5-29) > ProteoWizard Analysis: 2.1.2703 (2011-5-18) > Build date: May 29 2011 15:44:03 > > Thanks for your help, > Florian > |