Using subset of target peptides as iRT peptides

Using subset of target peptides as iRT peptides Erik  2022-02-23

Hi Skyline team,

I was wondering/trying to use a subset (12-15 peptides) of my SIS heavy peptides for two purposes; remaining it as an internal standard for my target light peptide but also as an iRT standard. This way I don't have to use an additional peptide spike-in that I have to measure.

Is this possible in skyline? Or will it mess up the iRT calculation and/or H:L ratio calculation?
If it is possible, what would be the best way to set-up this document?


Nick Shulman responded:  2022-02-23
You should try it. I think it will work.

A few times, people have wanted to use the same peptides for both iRT and for Global Standard normalization. That is a little tricky to do, because the Skyline user interface does not allow you to assign two different standard types to the same peptide. However, when the same iRT peptide appears multiple times in the document, only the first occurrence of that peptide is considered to be the iRT standard, and you can right-click on the second peptide and mark it as a global standard.

But, for what you are describing, I don't think it will be necessary to do the two-copies-of-a-peptide trick.

Let us know if you run into any problems.
-- Nick