Hello Soroush, Great! Good to verify that it is working as designed. And you will not miss those zero probability proteins; they would just add even more time to the processing and make a larger output file, but with no gain in high quality results.
Cheers, --Luis On Tue, Nov 17, 2020 at 9:32 PM Soroush F <sor...@gmail.com> wrote: > 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 > <https://groups.google.com/d/msgid/spctools-discuss/d8b7b05c-b808-47e7-a1bb-a4493749cfe4n%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/CACyS9bq-LiQiAGXXsGjKHUD%3DJ8yfVOLoJ9zK4Peh8jpDNDKXog%40mail.gmail.com.
