Hi Olga, While the best iProphet probability is saved per spectrum (also the PeptideProphet probability) in the case of multiple searches this is done for completeness of the pepxml file. We want to show you the best ID for each spectrum you search. However, when ProteinProphet runs in IPROPHET mode it considers each peptide sequence IDed in pepxml only once using the highest iProphet probability.
-David On Nov 22, 2011 6:06 AM, "olgas" <[email protected]> wrote: > Dear all > > In my iProphet output I get for each spectrum a separate iProphet > probability and I was wondering why, because in the iProphet paper it > says that "as the main outcome, iProphet permits the calculation of > more accurate posterior probabilities and FDR estimates at the level > of unique peptide sequences, where ONE probability is used for all > sequence identical PSMs observed [...]". What is now this one > probability? Is it just the highest of all the iProphet probabilities > for each peptide? > > Many thanks in advance! > > Olga > > -- > 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. > > -- 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.
