Hi Chris,
I assume the search results contain the actual amino acids in the matched peptides? i.e. if a substitution occurs, the search results report the matched peptide as containing the substituted amino acid residue. e.g. The FASTA lists:
PEPTIDER
But the search engine finds:
PEPTLDER
If this is the case, then you can add these peptides as targets using View > Spectral Libraries, selecting one, and clicking the Add button. Or clicking the Add All button.
I don't have an easy way to give you protein associations for these peptides which do not appear in the FASTA sequences, but this is a relatively easy way to get them into the Skyline Targets list.
Otherwise, you could also make your own list of matched peptide sequences with protein name associations in Excel and add them in Skyline through Edit > Insert > Peptides.
That's about all I can think of. Hope one of these is helpful to you in this case.
--Brendan