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 <liguilin...@gmail.com> 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. -- 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
