ICC-CLASS : isotopically-coded cleavable crosslinking analysis software suite




Petrotchenko, Evgeniy V.
Borchers, Christoph F.

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BioMed Central


Background: Successful application of crosslinking combined with mass spectrometry for studying proteins and protein complexes requires specifically-designed crosslinking reagents, experimental techniques, and data analysis software. Using isotopically-coded ("heavy and light”) versions of the crosslinker and cleavable crosslinking reagents is analytically advantageous for mass spectrometric applications and provides a “handle” that can be used to distinguish crosslinked peptides of different types, and to increase the confidence of the identification of the crosslinks. Results: Here, we describe a program suite designed for the analysis of mass spectrometric data obtained with isotopically-coded cleavable crosslinkers. The suite contains three programs called: DX, DXDX, and DXMSMS. DX searches the mass spectra for the presence of ion signal doublets resulting from the light and heavy isotopic forms of the isotopically-coded crosslinking reagent used. DXDX searches for possible mass matches between cleaved and uncleaved isotopically-coded crosslinks based on the established chemistry of the cleavage reaction for a given crosslinking reagent. DXMSMS assigns the crosslinks to the known protein sequences, based on the isotopically-coded and un-coded MS/MS fragmentation data of uncleaved and cleaved peptide crosslinks. Conclusion: The combination of these three programs, which are tailored to the analytical features of the specific isotopically-coded cleavable crosslinking reagents used, represents a powerful software tool for automated highaccuracy peptide crosslink identification. See: http://www.creativemolecules.com/CM_Software.htm


BioMed Central



Petrotchenko and Borchers: ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite. BMC Bioinformatics 2010 11:64.