I'm new to Skyline and trying to take advantage of Skyline's new capabilities to analyse crosslinked MS data. I crosslinked two proteins with DSS and added DSS as a modification in Settings>Peptide Settings>Modification>Edit modifications dialogue, also ticking the crosslinker box. However, if I select it as a modification and then import a FASTA file of my proteins, the crosslinked peptides do not show up as a potential entry. When I check the Modifications dialogue again, the box has been unchecked. I've noticed the box does not get unchecked if the crosslinker box is not checked.
Did i add the modification in the wrong place? Additionally, does Skyline produce all the potentially crosslinked peptide pairs like it produces peptides digested by Trypsin or do I need to provide that list?