Yes, it works in TPP 4.7.1. Thank you very much! 在 2014年10月16日星期四UTC+8上午3时49分16秒，David Shteynberg写道： > > Does this also happen when you try the latest pipeline? The current > released version is 4.7.1. > > Thanks, > -David > > On Wed, Oct 15, 2014 at 2:22 AM, 李桂林 <[email protected] <javascript:>> > wrote: > > 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! > >> > >> > >> > > -- > > You received this message because you are subscribed to the Google > Groups > > "spctools-discuss" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to [email protected] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at http://groups.google.com/group/spctools-discuss. > > For more options, visit https://groups.google.com/d/optout. >
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