Using same molecules as iRT standard and surrogate internal standards?

Using same molecules as iRT standard and surrogate internal standards? Will Thompson  2021-07-02

Hi Skyline Team,

I have a use case where i would like to use the same set of stable-isotope labeled molecules both as iRT standards as well as surrogate internal standards for the purposes of quantification. If i set the molecule as an iRT standard (i.e. the little "clock" icon comes up on the molecule) then when i go to the right-click menu to set that molecule as a surrogate standard the selections are greyed out. I can't think of any practical reason why this would not be allowed. Am I doing something wrong, is there a functional reason this is the case, or is this a bug?

Representative Skyline file attached. IF you look in the document grid, you do have the surrogate standards assigned to different molecules, but this is only because i did this part before applying the iRT correction.

Help as always is appreciated.



Nick Shulman responded:  2021-07-26

This issue was discussed over email and Brendan came up with this workaround:

I know it is fairly common to include peptides twice for the purpose of putting all the iRTs at the top but also including them in their proteinS when using endogenous iRTs, and I believe only the first instance shows up with the clock face indicating they are recognizing as iRT standards.

It would probably be tricky to fix this all of the way and have Skyline allow you to have multiple rules for the same molecule. It sounds like this workaround is sufficient for now.
-- Nick