How can I add a modification of amidation for synthetic peptides.
This is a loss of one O and a gain of one NH. Net loss of 0.9839 on the COOH terminus.
I tried making the modifications in peptide settings but it doesn't accept them.
Nick Shulman responded:
2023-11-16 12:13
Skyline actually already knows about the "Amidated (C-term)" modification.
If you go to:
Settings > Peptide Settings > Modifications
and push the "Edit List" button next to "Structural Modifications" and then push the "Add" button, you can then choose "Amidated (C-term)" in the "Name" dropdown.
Skyline will fill in the chemical formula with "NH-O" and will set the terminus to "C".
In Skyline, the chemical formula for something that includes a loss would be written as something with a minus sign in it such as "NH-O" where everything after the minus sign represents the atoms which are removed by the modification.
-- Nick