Someone else had a question about incorporating AiB into a peptide sequence:
https://skyline.ms/announcements/home/support/thread.view?rowId=64877

My recommendation was that they make it so that the peptide sequence has an "A" at the position where AiB would appear, and then apply a modification with the chemical formula "CH2" so that the modified amino acid would have the same formula as AiB.

When you are defining a modification, there are three options for "Terminus": blank, "N" and "C".
You should choose the blank option if you do not want Skyline to impose any restrictions on where the modified amino acid is allowed to appear in the peptide sequence.

We recommend the following webinar if you would like to learn more about working with modifications in Skyline:
https://skyline.ms/webinar10.url
-- Nick