Hello Brian, Thanks for the discussion. The way this is possible is because there are degenerate peptides that map to multiple proteins, in which case only those that have sufficient weight will be counted as "is contributing evidence" peptides. Only those PSM instances that are contributing evidence are counted in the "tot num peps" value. Please let me know if further clarification would be helpful or if you have other questions.
Cheers, -David On Wed, Jun 28, 2023 at 9:27 AM Hampton, Brian <bhamp...@som.umaryland.edu> wrote: > Hello David, > > I have difficulty understanding this. I had always operated under the > assumption that the "num unique peps" would be less than or equal to the > "tot num peps" - because - I thought "tot num peps" = "num unique peps" + > number of (shared) peptides also mapping to given protein. Is this not the > case and if so how would "tot num peps" ever be less than "num unique peps"? > > Best regards, > Brian > > > > Brian Hampton > Proteomics Core Lab > > Center for Vascular and Inflammatory Diseases > > University of Maryland School of Medicine > > BioPark One Rm 307 > > 800 West Baltimore Street > > Baltimore, MD. 21201 > > (410)706-8207 > ------------------------------ > *From:* 'David Shteynberg' via spctools-discuss < > spctools-discuss@googlegroups.com> > *Sent:* Wednesday, June 28, 2023 11:33 AM > *To:* spctools-discuss@googlegroups.com <spctools-discuss@googlegroups.com > > > *Subject:* Re: [spctools-discuss] ProteinProphet output number of unique > peptides vs total number of peptides > > Hi Murielle, > > Sorry this is a little confusing. Column "num unique peps" represents > total number of unique peptides mapping to the protein. The "tot num peps" > counts the PSMs that are "contributing evidence" (last column) to the > protein, sometimes this number can be lower because not all peptides > mapping are contributing evidence and spectral counts can be low per > peptide. > > The answer to your second question is *yes*, the "tot num peps" is the > spectral count for "is contributing evidence" peptides. > > Cheers, > -David > > > On Wed, Jun 28, 2023 at 7:27 AM muriell...@gmail.com < > murielle.al...@gmail.com> wrote: > > Hi David, > > Thank you for such a quick reply! > > I used tpp version 6.2.0 run via a singularity image and I produced the > table by including the EXCELXX option in proteinprophet. > > Cheers, > > Murielle > > On Wednesday, June 28, 2023 at 12:44:03 AM UTC+2 David Shteynberg wrote: > > Hi Murielle, > > Thanks for using the TPP and submitting your question here. When I try > the latest version of the TPP and run ProteinProphet through there, the > columns exported in my tab separated file from ProteinProphet are different > from yours. Can you please provide a bit more information about how you > generated this file and which version of the software you used? > > Cheers, > -David > > On Tue, Jun 27, 2023 at 7:10 AM muriell...@gmail.com <muriell...@gmail.com> > wrote: > > Hi all, > > I have two questions concerning the output of ProteinProphet : > > 1) Why do I have some entries for which the total number of peptides is > lower than the number of unique peptides? (see columns 5 and 6 below, an > extract of my output table) > > [image: protein prophet output.jpeg] > 2) Does the column "total number of peptides" correspond to spectral > counts? > > Thank you very much , > > Murielle > > -- > 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/be3b35c9-e308-4e35-8551-03425f7d1704n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/be3b35c9-e308-4e35-8551-03425f7d1704n%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/04691060-aedc-4d65-87a0-ae40aa92f889n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/04691060-aedc-4d65-87a0-ae40aa92f889n%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/CAGJJY%3D9cFy1deU1TrZzMRyJ7GqTX4ZX-bByL6GDFj6ZEcU6Kug%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D9cFy1deU1TrZzMRyJ7GqTX4ZX-bByL6GDFj6ZEcU6Kug%40mail.gmail.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/BL0PR03MB4259C80B5A47840AFEEB12948924A%40BL0PR03MB4259.namprd03.prod.outlook.com > <https://groups.google.com/d/msgid/spctools-discuss/BL0PR03MB4259C80B5A47840AFEEB12948924A%40BL0PR03MB4259.namprd03.prod.outlook.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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