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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