custom modidfication

custom modidfication edi goihberg  2019-01-11

we are trying to modify c terminal lysine on a peptide, the modification is unique in that it adds a permanent charge via quaternary ammonium ion
we tried creating the transition in silico using previous experimental data after adding the chemical formula at the modification setting the transition that we got did not correspond to the published experimental data probably since the double and single charge that the program creates is by adding a proton to the molecule while our peptide is already charged, is there a way to add a charge to the modification setting?
Thank you,

Brian Pratt responded:  2019-01-17

Hi Edi,

Skyline has a built in assumption that peptides are charged by (de)protonation. It's my understanding that this assumption is central to the model of how peptides fragment - sodiation [M+Na] for example would yield different fragments than protonation [M+H], and we only model the protonation case.

For generalized molecules, though, you can specify whatever kind of adduct you like. The downside is that we don't do fragmentation prediction on things that aren't peptides. You could probably work out a transition list for the fragments if you know what they're expected to be.

Thanks for using the Skyline support board!

Brian Pratt