Dear TPP developers, I might have uncovered a bug in ProteinProphet, or at least stumbled across a result which does not make sense to me. We are using all annotated isoforms from Swissprot when we search data from human. This roughly doubles the number of human entries from 20k to 40k many which as identical over long stretches. It seems I end up with protein groups of high probability but all members have a probability of 0. Is this expected:
<protein_group group_number="311" pseudo_name="50" probability="1.0000"> <protein protein_name="P05164" n_indistinguishable_proteins="5" probability="0.0000" ... ... <protein protein_name="P05164_CHAIN_2" n_indistinguishable_proteins="1" probability="0.0000" ... ... <protein protein_name="P05164_CHAIN_3" n_indistinguishable_proteins="1" probability="0.0000" ... ... <protein protein_name="P05164_CHAIN_4" n_indistinguishable_proteins="1" probability="0.0000" ... ... </protein_group> The result for the same data, same search parameters but with a database not containing isoforms I get: <protein_group group_number="26" probability="1.0000"> <protein protein_name="P05164" n_indistinguishable_proteins="1" probability="1.0000" percent_coverage="27.7" ... </protein_group> I would greatly appreciate if could tell me if this behavior is expected. Thanks! Lars Malmstroem ETH Zurich Switzerland -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
