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.
