P.S. Not all of them are 'charge 1 spectrum'. 在 2014年10月15日星期三UTC+8下午5时21分05秒，李桂林写道： > > Hi guys, > I want to use PeptideProphet in TPP v4.6.3 to parse my search result > which is generated by Tandem in TPP too. But I got a problem when I tried > the PeptideProphet. > Here is how I do this. > 1. database search against a target-decoy database > 2. transform the search result to pepXML using Tandem2XML in TPP > 3. run PeptideProphet with 'xinteract'. Command, 'path\to\xinteract > -Nout.pep.xml -p0 -l6 -OAP -Od -d###REV### input.pepXML' > > But I got warnings like > > 'Encoded charge of spectrum ** does not match the assumed_charge 1' > > and then the PeptideProphet stopped and reported error > > 'Iterations: error in getOrderedProb' > > I can successfully run the PeptideProphet before with my pipeline, but > now it doesn't work. > Can anybody put forward a resolution to me? Does the 'Charge 1' make > the difference? I found that almost the warnings are related to charge 1 > spectrum (assumed_charge 1). > > Thanks! > > > >
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