I am not sure I understand what you are asking.
If you want to know which peptides map to multiple proteins, you should use the menu item:
Refine > Associate Proteins
The Associate Proteins dialog has changed a lot in the most recent version of Skyline (22.2), and it gives you options about what to do with peptides which match to multiple proteins. I imagine you should check the checkbox that says "Create protein groups".
I am not sure what the best way is to find the peptides which were assigned to a protein group. One thing that you could do is use the Document Grid to find the peptides whose Protein Description starts with "Group of".
Does this answer your question?
-- Nick |
Hi Nick,
Yeah, sorry. Let me be more descriptive. That's my fault. I mean something like, can I highlight peptides in the Targets column that match to multiple protein entries in the background proteome versus the ones that are proteotypic? In my import, I'm allowing all peptides including the ones that match to multiple proteins, but I now just want to have a label that the individual tryptic peptide sequence is matching to multiple proteins. Does that make sense?
Best,
chris |