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ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite.
Petrotchenko EV, Borchers CH. Petrotchenko EV, et al. BMC Bioinformatics. 2010 Jan 28;11:64. doi: 10.1186/1471-2105-11-64. BMC Bioinformatics. 2010. PMID: 20109223 Free PMC article.
Isotopically coded cleavable cross-linker for studying protein-protein interaction and protein complexes.
Petrotchenko EV, Olkhovik VK, Borchers CH. Petrotchenko EV, et al. Mol Cell Proteomics. 2005 Aug;4(8):1167-79. doi: 10.1074/mcp.T400016-MCP200. Epub 2005 May 18. Mol Cell Proteomics. 2005. PMID: 15901824
BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics.
Petrotchenko EV, Xiao K, Cable J, Chen Y, Dokholyan NV, Borchers CH. Petrotchenko EV, et al. Mol Cell Proteomics. 2009 Feb;8(2):273-86. doi: 10.1074/mcp.M800265-MCP200. Epub 2008 Oct 6. Mol Cell Proteomics. 2009. PMID: 18838738
Use of a combination of isotopically coded cross-linkers and isotopically coded N-terminal modification reagents for selective identification of inter-peptide crosslinks.
Petrotchenko EV, Serpa JJ, Borchers CH. Petrotchenko EV, et al. Anal Chem. 2010 Feb 1;82(3):817-23. doi: 10.1021/ac901637v. Anal Chem. 2010. PMID: 20050626
An isotopically coded CID-cleavable biotinylated cross-linker for structural proteomics.
Petrotchenko EV, Serpa JJ, Borchers CH. Petrotchenko EV, et al. Mol Cell Proteomics. 2011 Feb;10(2):M110.001420. doi: 10.1074/mcp.M110.001420. Epub 2010 Jul 9. Mol Cell Proteomics. 2011. PMID: 20622150 Free PMC article.
Crosslinking combined with mass spectrometry for structural proteomics.
Petrotchenko EV, Borchers CH. Petrotchenko EV, et al. Mass Spectrom Rev. 2010 Nov-Dec;29(6):862-76. doi: 10.1002/mas.20293. Mass Spectrom Rev. 2010. PMID: 20730915 Review.
Use of proteinase K nonspecific digestion for selective and comprehensive identification of interpeptide cross-links: application to prion proteins.
Petrotchenko EV, Serpa JJ, Hardie DB, Berjanskii M, Suriyamongkol BP, Wishart DS, Borchers CH. Petrotchenko EV, et al. Mol Cell Proteomics. 2012 Jul;11(7):M111.013524. doi: 10.1074/mcp.M111.013524. Epub 2012 Mar 21. Mol Cell Proteomics. 2012. PMID: 22438564 Free PMC article.
Using multiple structural proteomics approaches for the characterization of prion proteins.
Serpa JJ, Patterson AP, Pan J, Han J, Wishart DS, Petrotchenko EV, Borchers CH. Serpa JJ, et al. Among authors: petrotchenko ev. J Proteomics. 2013 Apr 9;81:31-42. doi: 10.1016/j.jprot.2012.10.008. Epub 2012 Oct 17. J Proteomics. 2013. PMID: 23085224
Using isotopically-coded hydrogen peroxide as a surface modification reagent for the structural characterization of prion protein aggregates.
Serpa JJ, Makepeace KA, Borchers TH, Wishart DS, Petrotchenko EV, Borchers CH. Serpa JJ, et al. Among authors: petrotchenko ev. J Proteomics. 2014 Apr 4;100:160-6. doi: 10.1016/j.jprot.2013.11.020. Epub 2013 Dec 3. J Proteomics. 2014. PMID: 24316355
"Out-gel" tryptic digestion procedure for chemical cross-linking studies with mass spectrometric detection.
Petrotchenko EV, Serpa JJ, Cabecinha AN, Lesperance M, Borchers CH. Petrotchenko EV, et al. J Proteome Res. 2014 Feb 7;13(2):527-35. doi: 10.1021/pr400710q. Epub 2014 Jan 3. J Proteome Res. 2014. PMID: 24354799
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