Difference in unique PSMs between psm.tsv and protein.tsv

[Rakksor]

Hi,

Thanks for the great tool and documentation. I do have a question about the output files however:

I used FragPipe v 15.0 with MSFragger 3.2 and Philosopher 3.4.13 to analyze timsTOF data. When counting the number of unique PSMs per protein by selecting all PSMs for which the Is Unique column in psm.tsv is true I get a different number than in the Unique Spectral Count column in protein.tsv for some proteins. Specifically, some PSMs for which the Is Unqiue column in psm.tsv is false still seem to be counted in the Unique Spectral Count column in protein.tsv.

From the description in the Wiki I would have expected these two columns to match, is there any reason for this difference?

Thank you for your help
Beni

[prvst]

Hi Beni. Thanks for the kind words. We found an issue that affected the counts in the protein table, and we will have a new version released soon. For now, please consider the PSM table as being correct.

[Rakksor]

Hi Felipe,

Thanks a lot for the quick answer! I'll use the values in psm.tsv then.

Cheers
Beni