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

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Petrotchenko, Evgeniy V ^a   Borchers, Christoph H ^a  

^a UNIVERSITY OF VICTORIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS SOFTWARES; CROSS-LINKING REAGENTS; DATA ANALYSIS SOFTWARES; EXPERIMENTAL TECHNIQUES; MASS SPECTROMETRIC DATA; MS/MS FRAGMENTATION; POWERFUL SOFTWARE TOOLS; PROTEIN COMPLEXES;

APPLICATION PROGRAMS; MASS SPECTROMETERS; MASS SPECTROMETRY; PEPTIDES;

CROSSLINKING;

CROSS LINKING REAGENT; ISOTOPE; PEPTIDE; PROTEIN;

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; ISOTOPE LABELING; MASS SPECTROMETRY; METHODOLOGY; PROTEIN DATABASE; PROTEOMICS;

CROSS-LINKING REAGENTS; DATABASES, PROTEIN; ISOTOPE LABELING; ISOTOPES; MASS SPECTROMETRY; PEPTIDES; PROTEINS; PROTEOMICS; SOFTWARE;

EID: 77249179311     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-64     Document Type: Article

References (16)

1. Sinz A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom Rev 2006, 25:663-682. 10.1002/mas.20082, 16477643.
2. Müller DR, Schindler P, Towbin H, Wirth U, Voshol H, Hoving S, Steinmetz MO. Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis. Anal Chem 2001, 73:1927-1934. 10.1021/ac001379a, 11354472.
3. Bennett KL, Kussmann M, Björk P, Godzwon M, Mikkelsen M, Sørensen P, Roepstorff P. Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping--a novel approach to assess intermolecular protein contacts. Protein Sci 2000, 9:1503-18. 10.1110/ps.9.8.1503, 2144725, 10975572.
4. Petrotchenko EV, Olkhovik VK, Borchers CH. Isotopically coded cleavable cross-linker for studying protein-protein interaction and protein complexes. Mol Cell Proteomics 2005, 4:1167-1179. 10.1074/mcp.T400016-MCP200, 15901824.
5. ProteinProspector. , http://prospector.ucsf.edu
6. Tang Y, Chen Y, Lichti CF, Hall RA, Raney KD, Jennings SF. CLPM: a cross-linked peptide mapping algorithm for mass spectrometric analysis. BMC Bioinformatics 2005, 6(Suppl 2):S9. 10.1186/1471-2105-6-S2-S9, 1637035, 16026606.
7. de Koning LJ, Kasper PT, Back JW, Nessen MA, Vanrobaeys F, Van Beeumen J, Gherardi E, de Koster CG, de Jong L. Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes. FEBS J 2006, 273:281-291. 10.1111/j.1742-4658.2005.05053.x, 16403016.
8. Schilling B, Row RH, Gibson BW, Guo X, Young MM. MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J Am Soc Mass Spectrom 2003, 14:834-850. 10.1016/S1044-0305(03)00327-1, 12892908.
9. MS3D collaboratory. , http://ms3d.org
10. Gao Q, Xue S, Doneanu CE, Shaffer SA, Goodlett DR, Nelson SD. Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry. Anal Chem 2006, 78:2145-2149. 10.1021/ac051339c, 16579592.
11. Anderson GA, Tolic N, Tang X, Zheng C, Bruce JE. Informatics strategies for large-scale novel cross-linking analysis. J Proteome Res 2007, 6:3412-3421. 10.1021/pr070035z, 2475505, 17676784.
12. Seebacher J, Mallick P, Zhang N, Eddes JS, Aebersold R, Gelb MH. Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing. J Proteome Res 2006, 5:2270-2282. 10.1021/pr060154z, 16944939.
13. Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R. Identification of cross-linked peptides from large sequence databases. Nat Methods 2008, 5:315-318. 10.1038/nmeth0808-748a, 2719781, 18327264.
14. Jin Lee Y. Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes. Mol Biosyst 2008, 4:816-23. 10.1039/b801810c, 18633483.
15. Yu W, Vath JE, Huberty MC, Martin SA. Identification of the facile gas-phase cleavage of the Asp-Pro and Asp-Xxx peptide bonds in matrix-assisted laser desorption time-of-flight mass spectrometry. Anal Chem 1993, 65:3015-3023. 10.1021/ac00069a014, 8256865.
16. Petrotchenko EV, Xiao K, Cable J, Chen Y, Dokholyan NV, Borchers CH. BiPS, a photo-cleavable, isotopically-coded, fluorescent crosslinker for structural proteomics. Mol Cell Proteomics 2009, 8:273-286.