• Sign In
  1. Requests

trouble shooting : adding a background proteome

support

View Request

view list print
trouble shooting : adding a background proteome ssedigh2  2024-12-09 13:45
 

Hi Skyline team ,

I am having a bit of trouble adding the background proteome to a skyline document.
I have downloaded a Fast fie from Uniprot , and than in Skyline document I go to Setting >Peptide Setting >Digestion tab and add the background proteome . how ever in my target list the peptides are not assigned to the proteins as they should be . Can you help me fix this ?

P.S. The skyline document is for a Surequant Assay on there samples . So the peptides of interest and the the heavy and light precursors are in the list of targets .

Thank you for your continued support,
Best,
Sogol
 
 
Nick Shulman responded:  2024-12-09 15:01
If you want your peptides to be assorted into the proteins that they belong to, the menu item that you should use is:
Refine > Associate Proteins

The background proteome is mostly used for keeping track of things that are in your sample which you are not interested in. For this reason, the "Enforce uniqueness by" is probably the most useful background proteome feature.

For grouping peptides by their protein the "Refine > Associate Proteins" menu item is the best.
-- Nick