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


CONCLUSIONS
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.
Petrotchenko
Evgeniy V
EV
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, Canada.
Borchers
Christoph H
CH
D003432:Cross-Linking Reagents / Q000737:chemistry*; D030562:Databases, Protein; D007553:Isotope Labeling; D007554:Isotopes / Q000737:chemistry; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software
D003432:Cross-Linking Reagents; D007554:Isotopes; D010455:Peptides; D011506:Proteins