People have asked a number of times over the years for Skyline to remove the protein N-terminal Methionine from the protein N-terminal peptide. Most recently in this support request:

https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?rowId=24953

Since you are currently working in the Peptide Settings - Digestion tab, maybe you could find a way to add a checkbox near the Enzyme dropdown list that causes Skyline to perform this removal when checked. It would have to impact the background proteome as well as PeptideGroup.GetPeptides().

Requested again by a new user. I still think the ckeckbox on the Digestion tab is the right idea. Not higher priority than your current work, but a little higher priority with a second request. Wish we had more time from interns that could handle something like this.