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Open Access Software

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

Evgeniy V Petrotchenko and Christoph H Borchers*

Author Affiliations

University of Victoria - Genome British Columbia Protein Centre, Department of Biochemistry & Microbiology, University of Victoria, #3101-4464 Markham Street, Vancouver Island Technology Park Victoria, BC V8Z7X8, Canada

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BMC Bioinformatics 2010, 11:64  doi:10.1186/1471-2105-11-64

Published: 28 January 2010

Abstract

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 high-accuracy peptide crosslink identification. See: http://www.creativemolecules.com/CM_Software.htm webcite