Several people have asked for the ability to add not fully cleaved peptides with association to the source protein. This could be done in the Edit > Insert > Peptides form when both the peptide and protein name are given with a background proteome. Then the protein could be queried from the background proteome file, and searched for the matching sequence.

Weren't you going to look at this for Jarrett at one point for allowing background proteome matching for both N- and C-terminal semi-cleavage?

This got fixed back in February 2017.