Hi Emma, Yes, for spectral counting of proteins it seems appropriate to consider only "is contributing evidence" peptides, "tot num peps" would be the value to use.
Cheers, -David On Wed, Jun 28, 2023 at 9:35 AM Emma Whittington <[email protected]> wrote: > I am also a little confused/requiring clarification. For label-free > quantification would you use the "tot num peps" for spectral counts when > calculating something like NSAF? From your description, it sounds like > that's the total number of contributing spectra. > > all the best, > Emma > On Wednesday, 28 June 2023 at 18:27:48 UTC+2 Hampton, Brian 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 <(410)%20706-8207> >> ------------------------------ >> *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/f5e7ab0f-7f2a-4494-8560-652629ef9812n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/f5e7ab0f-7f2a-4494-8560-652629ef9812n%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%3D-g9t5_%3DwPA9dJhqtzTuV_d1VF1MW9AztfC3DtNNbSQCw%40mail.gmail.com.
