highlighting peptides that map to multiple proteins

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highlighting peptides that map to multiple proteins cabarnescabarnes  2022-09-30
 

Hi all,

Simple question, but is there a way to highlight which peptides are matching to multiple proteins? I have a proteogenomics type of effort going on and there is utiility in me finding protein evidence for multiple isoforms that might all individually have the same tryptic peptide, but that tryptic peptide may only map to that novel isoform group and nothing else, which would be helpful in and of itself for me as I want to keep all of the isoforms in there.

Best,

chris

 
 
Nick Shulman responded:  2022-10-03
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
 
cabarnescabarnes responded:  2022-10-04
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