Hi Brian, I just confirmed in the code that it is counted here when the weight of the peptide is minimum 0.5 and the probability minimum 0.2.
Cheers, -David On Wed, Jun 28, 2023 at 9:49 AM Hampton, Brian <[email protected]> wrote: > Hi David, thanks for the quick reply. > > I think I see now. When there is some ambiguity which prevents > determining a precise peptide sequence, for example incomplete fragment ion > series, or isobaric AA assignments etc. then there must be a probability > calculation performed, the result of which attempts to assign this peptide > to the more likely protein candidate. The result of which is recorded in > the "total num peptides" value. In the case of a tie, is the value added > to all possible protein hits or not used? > > Thanks a bunch! > > Brian > ------------------------------ > *From:* 'David Shteynberg' via spctools-discuss < > [email protected]> > *Sent:* Wednesday, June 28, 2023 12:37 PM > *To:* [email protected] <[email protected] > > > *Subject:* Re: [spctools-discuss] ProteinProphet output number of unique > peptides vs total number of peptides > > 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 <[email protected]> > 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 < > [email protected]> > *Sent:* Wednesday, June 28, 2023 11:33 AM > *To:* [email protected] <[email protected] > > > *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 [email protected] < > [email protected]> 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 [email protected] <[email protected]> > 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 [email protected]. > 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 [email protected]. > 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 [email protected]. > 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 [email protected]. > 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. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8eH7q7L7moDYWT7vgmgJrFtJpdyyS4ZZbuX4Ygy9utuQ%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8eH7q7L7moDYWT7vgmgJrFtJpdyyS4ZZbuX4Ygy9utuQ%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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/BL0PR03MB42598ECFAC9E9948FA1D53908924A%40BL0PR03MB4259.namprd03.prod.outlook.com > <https://groups.google.com/d/msgid/spctools-discuss/BL0PR03MB42598ECFAC9E9948FA1D53908924A%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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