To add a comment: the phenomenon happens for a few of the most abundant proteins, having many peptides. The peptide abundances look OK in the quantitation.tsv file, so I may be able to work around this by recalculating the ratios from this file.
Magnus On Wednesday, 8 August 2018 15:18:33 UTC+2, magnus....@gmail.com wrote: > > Dear TPP Team, > > I am processing some TMT-10 data, and observed a strange behavior for some > proteins (see example). Although I am getting good quantitative information > on the peptide level for many peptides, no quantitative information is > reported on the protein level for this and a few other proteins. The > peptides with all zeroes have no TMT-signal in the MS3 spectrum despite a > strong ID from the MS2, so they are correct. Other proteins with some > peptides having all zeroes from Libra do produce protein-level Libra > results in the same analysis. the LIBRA9 and LIBRA10 channels are negative > controls, and should be empty (or at least much lower than LIBRA1-8). > Overall, the results agree well with MaxQuant, so I don't think it is a > major or systematic issue at all. > > In the quantitation.tsv, many of the peptides with non-zero quantitation > are kept ("Yes" in the "kept?" column), but the protein ratios > (protratio0-9) are still all zero! > > I used default settings in PeptideProphet and ProteinProphet, except for > selecting a TMT-10 conditions file for Libra (with SRS data turned on) in > TPP v5.1.0 Syzygy, Build 201711031215-7670 (Windows_NT-x86_64). > > Any ideas? > > > Cheers, > > Magnus > > > -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.