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How to specify simultanous structural modification for N-term and for a side chain, if the modified sidechain is on the N-terminal amino acid

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How to specify simultanous structural modification for N-term and for a side chain, if the modified sidechain is on the N-terminal amino acid pavel shliaha  2024-04-24 14:31
 

I have two static (structural modifications):

  1. The N-terminus of the peptide is modified by phenylisocyanite.
  2. The NH2 group of Lys is modified by propionyl group.

it so happens that I have a peptide that has K on the N-terminus:

KQLATKAAR

meaning the first Lys should have both phenylisocyanite and propionyl

how ever when loading the peptide in skyline only adds propionyl, ignoring phenylisocyanite

if I however add Ala to the peptide N terminus

AKQLATKAAR

I do get A modified with phenylisocyanite and Lys with propionyl.

How do I force skyline to add both structural modifications to K in KQLATKAAR?
 
 
Nick Shulman responded:  2024-04-24 14:38
Skyline only allows you to put one modification on any particular residue so you will have to go to:
Settings > Peptide Settings > Modifications
and define a single modification which has a chemical formula which is the combination of the two modifications that you want to have on that N-terminal amino acid.
-- Nick