title: Application of a fast sorting algorithm to the assignment of mass spectrometric cross-linking data.
abstract: 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.
authors.affiliation: University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada.
authors.forename: Evgeniy V
authors.initials: EV
authors.lastname: Petrotchenko
authors.forename: Christoph H
authors.initials: CH
authors.lastname: Borchers
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides / Q000032:analysis* / Q000737:chemistry*; D011506:Proteins / Q000032:analysis* / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides; D011506:Proteins
keywords: Bioinformatics; Crosslinking; Peptides; Protein complexes; Proteins