Hi, We're running TPP v4.3 rev1 and I have a question about ProteinProphet. We just ran into a case where an I->L exchange in a peptide made the difference between two isoforms. ProteinProphet claims it took this into account, "residue_substitution_list=I -> L" in the protXml header, but I don't see evidence the substitution was considered; if it were, the isoform with fewer peptides should have been subsumed. As a result, both isoforms were identified with protein_probability=1.
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