Cys occupancy and peptide inclusion

Cys occupancy and peptide inclusion Stella  2022-06-17

Hi everyone!

I have a simple question: I am working with compounds that react covalently to Cys on targeted proteins and I would like to ask if there is a way to automatically selected peptides containing Cys, similarly to the "Exclude peptides containing" in the Peptide Settings.

Thank you very much!

Nick Shulman responded:  2022-06-17
I don't think there is a way to do that but you could use the Document Grid to delete all peptides from your document which do not contain a Cysteine.

View > Document Grid
Choose "Peptides" from the Reports dropdown at the top of the Document Grid
Right-click on the "Peptide Modified Sequence" column and choose "Filter"
Choose "Does not contain" and type "C" in the textbox.
Click the square in the top left corner of the Document Grid to select all rows.
Click the red X on the toolbar at the top of the Document Grid.

In other situations you might have rules about which peptides to keep which end up being too complicated to do with filtering in the Document Grid. In cases like that, you might be able to generate the list of peptides that you want in some other tool and then use the menu item: "Refine > Accept Peptides" to delete all the peptides except the ones in your list.
-- Nick