Dear Bjorn, Thanks so much for your reply.
Yes, I understand that the initial peptide probability will be adjusted to take into account of sibling peptides -> nsp adjusted probability. I was referring to the initial probability itself. And we've possibly just found out why through some tests. Our Protein Prophet step was done with a number of input files, from Inter Prophet. Although Inter Prophet is meant to combine results before running them into Protein Prophet, we are unable to combine all the results as there were too much data. Hence, results were split into a number of Inter Prophet files. When these files were processed in a single Protein Prophet run, peptides that were only found in one of the Inter Prophet files were given a lower initial peptide probability. When only the particular Inter Prophet file was selected for a Protein Prophet run, the initial peptide probability reported for the peptide is correct. Cheers Eric On Nov 13, 11:14 pm, Bjorn <[email protected]> wrote: > Hi Eric, > If I'm not mistaken, the ProteinProphet "re-evaluates" the peptide > probabilities based on the number of sibling peptides > (NSP).http://www.proteomecenter.org/2010.OCT/Seattle%20Course%20Pack.pdf > (pages 92-93 answer your question) > > Hope this helps, > > Cheers, > Bjorn -- 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.
