Hi Skyline Team,

I have been hoping to be able to remove repeated peptides in certain ways in Skyline for a long time. Recently, I saw the discussion in issue #861, and I would like to chime in.
I wonder if Skyline can integrate ProteinProphet or to read the prot.xml from ProteinProphet, and then have an option to remove/export the repeated peptides/empty proteins. Alternatively, Percolator also does protein inference now. Percolator wiki Maybe this can be an option for MSAmanda search.

Regards
Ho-Tak