This tool calculates fragment ion transitions for cross-linked peptide pairs. These can be used for PRM and SRM experiments. The program calculates the m/z values for the theoretical fragment ions including the full length released peptides, long arm ions resulting from the cleavage of a single PIR labile bond, and the b-type and y-type ions from both cross-linked peptides assuming both PIR labile bonds were cleaved. For non-cleavable cross-linkers, intact precursor m/z ions and b-type and y-type fragment ions are reported.
