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. © 2014 by John Wiley & Sons, Inc.

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

“…For MS/MS, the collision energy was set to 35%. Data were analyzed using the DXMSMS Match program from our ICC-CLASS (Isotopically Coded Cleavable Cross-Linking Analysis Software Suite), or with Kojak ( 47 ). For scoring and assignment of the MS/MS spectra, b and y ions were primarily used, with additional confirmation from collision-induced dissociation cleavage of the cross-linker, whenever this was available.…”

Protein unfolding as a switch from self-recognition to high-affinity client binding

“…Proteome Discoverer (version 1.4.0.288) was used to generate.MGF files from.RAW files. Data analysis was performed using DXMSMS Match 50 of ICC-CLASS 51 and 14 N 15 N DXMSMS Match 52 .…”

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker

“…We describe a CLMS workflow that improves upon previously published workflows in terms of detection, acquisition, and identification of crosslinked peptides (22,(24)(25)(26). This study yielded a rich crosslinking dataset, revealing hundreds of intra-and inter-molecular protein-protein interactions within the mitochondrial organelle.…”