two heavy labelled standards for one peptide

two heavy labelled standards for one peptide m teusel  2021-04-19

Dear Skyline Team,

I am using Skyline (64-bit) version
I have two different kinds of heavy isotope labelled standards: one 15N-labelled recombinantly produced protein and additionally a 15N13C-Arg synthetic peptide. Is there any option to have both heavy standards for my peptide together? At the moment I have an extra peptide for each sort of heavy label, which is fine to quantify light, but to compare the two heavy standards I have troubles as I would have to pick the same peak boundaries manually.
Optimally for this case I'd have one peptide with light and then two versions of heavy all displayed in one plot.

Thank you so much in advance.

Brendan MacLean responded:  2021-04-19

Absolutely. This was an early requirement for Skyline, because the funding organization, CPTAC, wanted to do this in their experiments as well. You can find Skyline documents with their examples here:

The 9.2 experiments used both 15N12C-Arg/Lys and all-15N labeled peptides.

Just quickly, when you drop the "Isotope label type" list, you can see an "<Edit list...>" option. You use that option to add label types to the default "heavy".

There is also a webinar on working with modifications in Skyline:

This case and the CPTAC data are presented around 51 minutes.

Hope this helps. Thanks for posting this question to the Skyline support board.


m teusel responded:  2021-04-19

Thanks a lot for the super quick reply. It works and makes my analyses so much easier - great!