Dear Luis, Thanks so much for your insight. It is very much appreciated.
I can see that the proteins that are not outputted in the ProteinProphet have PeptideProphet probability of <0.05. All the best, Soroush On Tuesday, November 17, 2020 at 2:42:17 PM UTC-5 Luis wrote: > Hello Soroush, > > ProteinProphet has baked-in defaults in the code that will skip over any > peptide with (initial) probability < 0.05 (and won't use those below 0.20 > post-NSP adjustment). Do any of those peptides that point to the missing > proteins violate that rule? > > This is certainly something that can be changed in the code on your local > copy, but it is not recommended. > > Cheers, > --Luis > > > > On Mon, Nov 16, 2020 at 6:31 PM Soroush F <sor...@gmail.com> wrote: > >> Dear all, >> >> I noticed that not all the proteins that exist in my PeptideProphet file >> will appear in the ProteinProphet output. Obviously I expect some proteins >> to be determined as having very low probability by the ProteinProphet, but >> why they don't appear in the ProteinProphet altogether? How can I keep them >> in the output of the ProteinProphet? >> >> Also, I am not setting anything to be excluded in the ProteinProphet >> setting (which I run through TPP). >> >> Many thanks for your help. >> >> Soroush >> >> -- >> 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 spctools-discu...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/7f2700a6-ec5a-42b1-b6b1-835e4e48c799n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/7f2700a6-ec5a-42b1-b6b1-835e4e48c799n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/d8b7b05c-b808-47e7-a1bb-a4493749cfe4n%40googlegroups.com.
