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Proteomics. 2014 Sep;14(17-18):1987-9. doi: 10.1002/pmic.201300486. Epub 2014 Jul 10.

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

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University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada.


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.


Bioinformatics; Crosslinking; Peptides; Protein complexes; Proteins

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