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 |