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Application of a fast sorting algorithm to the assignment of mass spectrometric cross‐linking data

Cross‐linking combined with MS involves enzymatic digestion of cross‐linked proteins and identifying cross‐linked peptides. Assignment of cross‐linked peptide masses requires a search of all possible binary combinations of peptides from the cross‐linked proteins’ sequences, which becomes impractical with increasing complexity of the protein system and/or if digestion enzyme specificity is relaxed. Here, we describe the application of a fast sorting algorithm to search large sequence databases for cross‐linked peptide assignments based on mass. This same algorithm has been used previously for assigning disulfide‐bridged peptides (Choi et al., ), but has not previously been applied to cross‐linking studies.