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

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.