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!