Peptide Uniqueness

Peptide Uniqueness Hui  2020-06-02

Hello Skyline Team,

Hope all is well.

I am trying to create an SRM list where we have human samples with mouse heavy standard. Is there a function that works the opposite of "Exclude Background Proteome" under "Edit -> Unique Peptides..."? The goal is to choose peptides that are shared between both human and mice genomes.

Thank you!

Brendan MacLean responded:  2020-06-02

Hi Hui,
You might try working backwards by:

  1. Add everything
  2. Paste the list of peptides to Excel
  3. Add a unique by organism constraint
  4. Paste the list of peptides to Excel
  5. In Excel use formula like this in column C =IF(COUNTIF(B$1:B$3,A1)>0,A1,"") on the range of unique by organism peptides in column B
  6. Copy paste the text of column C to a text editor and use Find and Replace to remove the empty rows
  7. Refine > Accept Peptides and paste your list of non-unique peptides into the form and OK

Something along these lines may get you what you are looking for.