A crosslink modification, or crosslinker, is a chemical that binds to the surface amino acids of proteins. It can attach to two different amino acids in close proximity, whether they are on the same protein or on different proteins. You use a crosslinker to map the structure and function of proteins and to find proteins that interact with each other.
The XlinkX algorithm1) identifies chemically crosslinked peptides. It supports different types of crosslinkers, including heterobifunctional.
Unlike other crosslink identification algorithms, the XlinkX algorithm uses the peptide fragment masses after the fragmentation of a cleavable crosslinker. For cleavable crosslinkers, it derives the masses of the two crosslinked peptides from the crosslink fragment peaks. As a result, you do not need to try all combinations of peptides of a complete proteome to find the two peptides that form the crosslinker. The algorithm converts the n2 growth of the search space with the number of peptides searched into a problem with linear growth of a sequence database search algorithm.
The XlinkX algorithm, developed by Fan Liu and Richard Scheltema in Albert Heck's group at Utrecht University, is licensed to Thermo Fisher Scientific.