Feature request: Add Indistinguishable Proteins column also to psm, ion and peptide tables

[hollenstein]

Dear FragPipe Team,

Is your feature request related to a problem? The requested feature is only for convenience. Currently the psm.tsv, ion.tsv, and peptide.tsv tables (and the combined versions of them) contain the column “Mapped Proteins”, to indicate all proteins a peptide maps to. In the end, however, a peptide is assigned to one protein or multiple proteins, when they are indistinguishable proteins. Looking at the peptide table, if there are entries in “Mapped Proteins” it is not clear if these proteins are indistinguishable proteins or a peptide maps to different protein “groups”. This becomes only evident from the protein table, when there are entries in the “Indistinguishable proteins” column or not.

Also, sometimes a protein of high interest is not the first one reported, i.e. it’s present in the Indistinguishable proteins but a different protein is reported in the “Protein” column. If one needs to extract the peptide information for such proteins (e.g. for making a summary) and there are multiple entries in the “Mapped Proteins” column, it's not clear if the peptide was actually assigned as a razor peptide to the protein of interest or not.

In both cases it's necessary to parse the protein table, create a mapping of the “Protein” and “Indistinguishable proteins”, and add this information back to the peptide table (or ion, psm, whatever is required).

Describe the solution you'd like Would it be possible to add the column “Indistinguishable proteins” also to all of the other tables?

Best, David