ICC-CLASS : isotopically-coded cleavable crosslinking analysis software suite
Date
2010-01-28
Authors
Petrotchenko, Evgeniy V.
Borchers, Christoph F.
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
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 highaccuracy
peptide crosslink identification. See: http://www.creativemolecules.com/CM_Software.htm
Description
BioMed Central
Keywords
UVic Genome BC Proteomics Centre
Citation
Petrotchenko and Borchers: ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite. BMC Bioinformatics 2010 11:64.