Import a large # of peptides with heavy isotope labels on c-terminal residue

Import a large # of peptides with heavy isotope labels on c-terminal residue wangqingok  2022-04-03

Hi Skyline Expert Team,

I am trying to import a large number of peptide sequences. After the import, I then chose the "modifications" to have a heavy K/R, and then all the K/R are highlighted in blue. But I only want to have the C-terminal K or R to be heavy labeled, but leave the internal K/R to be just light. Is there anyway to specify a modification position, not only on a certain residue but also a location of it? Such as "C terminal".

Or is there a way to allow me to modify the peptide sequence that will be imported to have a label such as [C13N15] near by the residue that I am going to specify as heavy and can skyline recognize such "C13N15" string and take is as a dedicated modification on this peptide? Thank you so much!

Nick Shulman responded:  2022-04-03
Yes, when you are defining a modification in Skyline, on the Edit Isotope Modification dialog there is a "Terminus" dropdown where you can choose "C" or "N" or leave blank if the modification should apply to all matching residues.

If you are choosing one of the modifications that Skyline already knows about, there are C-term variants of the common modifications. So, you could choose either the modification named "Label:13C(6)15N(2) (K)" or the modification named "Label:13C(6)15N(2) (C-term K)".

The way to tell Skyline about your isotope modifications is to go to:
Settings > Peptide Settings > Modifications
and press the "Edit List" button next to the "Isotope Modifications" listbox in the bottom half of the form. In the Edit Isotope Modifications dialog you can push the "Add" button and then either define a new modification by specifying its chemical formula, etc., or choose one of the predefined modification names that Skyline already knows about.

If you would like to learn more about modifications in Skyline you might find this webinar useful:
-- Nick