title: DXMSMS Match Program for Automated Analysis of LC-MS/MS Data Obtained Using Isotopically Coded CID-Cleavable Cross-Linking Reagents.
abstract: Cross-linking combined with mass spectrometry for the study of proteins and protein complexes is greatly facilitated by the use of isotopically coded cleavable cross-linking reagents. The isotopic coding of the cross-linker enables confident detection of the cross-link signals, while cleavage of the cross-linker provides masses of the individual peptides composing the cross-link and, therefore, facilitates unambiguous assignment of the cross-links. Here, we describe the DXMSMS Match program, designed for automatic analysis of LC-MS/MS mass spectrometric data obtained with isotopically coded CID-cleavable cross-linkers. The program verifies the assignments of the cross-links by precursor mass and by inspection of the MS/MS spectra for the fragments and the cleavage products of the cross-linked peptides. The program produces nonprobabilistic scores for matching the spectra to the theoretical fragmentation of the cross-links and a visual interface for the validation of the mass spectral matches.
authors.affiliation: University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, Canada.
authors.forename: Evgeniy V
authors.initials: EV
authors.lastname: Petrotchenko
authors.affiliation: University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, Canada.
authors.forename: Karl A T
authors.initials: KAT
authors.lastname: Makepeace
authors.affiliation: University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, Canada.|Department of Biochemistry & Microbiology, University of Victoria, University of Victoria, Victoria, Canada.
authors.forename: Christoph H
authors.initials: CH
authors.lastname: Borchers
mesh_terms: D001331:Automation; D003432:Cross-Linking Reagents / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D003432:Cross-Linking Reagents
keywords: cross-linking; mass spectrometry; software; stable isotope labeled cross-linkers