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.


On Wednesday, 8 August 2018 15:18:33 UTC+2, 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

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