December 2009

Cross-linking Analysis Made Easy

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Chemical cross-linking is a well-established method of studying protein-protein interactions, and, when combined with mass spectrometric analysis of the cross-linked proteins, it can be a powerful approach to probe the topologies and interacting surfaces of protein assemblies. However, comprehensive analysis of cross-linked peptides and protein assemblies is challenging, as most cross-linking reagents react with multiple residues and the solvent, which can inactivate the reactive groups and lead to “dead-end” links. The high complexity of cross-linked samples requires tandem mass spectrometric fragmentation data for confident identification, as available bioinformatic tools for automatic analysis of cross-linked spectra are far from robust. The researchers behind this study, however, demonstrate a new bioinformatic approach that may change that. Using multiple program modules within the Protein Prospector software package, they developed a strategy that greatly facilitates the discovery of cross-linked peptides in chemical cross-linking studies, allowing for results from a single data set. 

Biobit 4
Structure and low-energy CID spectrum of the cross-linked species with an m/z value of 670.854+ from a digest of an ecotin dimer; the cross-linker bridge is shown in green.

Finding Chimeras: A Bioinformatic Strategy for Identification of Cross-linked Peptides 

Feixia Chu, Peter R. Baker, Alma L. Burlingame and Robert J. Chalkley

Mol. Cell. Proteomics, published online Oct. 6, 2009 

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