Hi Lars and Andreas, In large protein groups this is expected behavior since the peptides are highly degenerate and their weights drop below the 0.5 cutoff required to compute a probability for any one given protein. There is an option for ProteinProphet called GROUPWTS that will use the sum of the weights among all proteins within the group for a given peptide to determine if the peptide will be used to compute a probability. With this option your grouped proteins should now have a probability to allow a secondary ranking among proteins within a group.
-David On Thu, Oct 25, 2012 at 7:30 AM, Andreas Quandt <[email protected]>wrote: > 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.
