Currently, Skyline makes it possible to exclude ragged end peptides from consideration for peptide targets, but it does not store information on the peptides that result when this option is not used to be able to know if a peptide results from a ragged end cleavage.
It would be nice to have this stored on the Peptide class, with the value available in reports. Apparently a reviewer requested the value from at least one investigator.
https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?rowId=3280