Hello David, Thanks very much for your response. Your slides from a TPP course (a couple of years old, now) state that iProphet's NSP model "Should be turned off when ProteinProphet NSP model is used". Is this still the recommendation? In the post I originally linked to, wrt NSP in iProphet and ProteinProphet, you state that you "have not found the two to interfere" which reads to me like it can be used in both.
John On Friday, February 19, 2016 at 2:24:06 PM UTC-5, David Shteynberg wrote: > > Hello John, > > Thank you for your question. > > NSP in iProphet looks at all proteins that a given peptide matches, it > then sums the probabilities of all the other peptides that match the same > protein. For a given peptide it then takes as the NSP the maximum such sum > over all the proteins matched. It is a bit different from NSP in > ProteinProphet since in ProteinProphet a given peptide has a different NSP > in each protein it appears. > > -David > > On Fri, Feb 19, 2016 at 11:04 AM, John Damask <[email protected] > <javascript:>> wrote: > >> Hi, >> >> I'm interested in learning more about how iProphet's NSP model works. The >> original paper doesn't discuss it as a first class iProphet model and Fig1 >> only shows it in ProteinProphet. >> >> In this post >> <https://groups.google.com/forum/#!searchin/spctools-discuss/iprophet$20nsp/spctools-discuss/mLAMdJUP8AQ/wGQfI0061scJ> >> >> David states "I have found that applying the NSP model at the iProphet step >> greatly improves performance on peptide level". But what is it doing, >> exactly? >> >> Thanks for providing such great software to the community! >> John >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
