DXMSMS Match Program for Automated Analysis of LC-MS/MS Data Obtained Using Isotopically Coded CID-Cleavable Cross-Linking Reagents

Curr Protoc Bioinformatics. 2014 Dec 12:48:8.18.1-8.18.19. doi: 10.1002/0471250953.bi0818s48.


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.

Keywords: cross-linking; mass spectrometry; software; stable isotope labeled cross-linkers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Automation*
  • Cross-Linking Reagents / chemistry*
  • Tandem Mass Spectrometry / methods*


  • Cross-Linking Reagents