A review of COFRADIC techniques targeting protein N-terminal acetylation

BMC Proceedings - Tập 3 Số S6 - 2009
Petra Van Damme1, Jozef Van Damme1, Hans Demol1, An Staes1, Joël Vandekerckhove1, Kris Gevaert1
1Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium;

Tóm tắt

Abstract Acetylation of nascent protein Nα-termini is a common modification among archae and eukaryotes and can influence the structure and function of target proteins. This modification has been studied on an individual protein or (synthetic) peptide level or on a proteome scale using two-dimensional polyacrylamide gel electrophoresis. We recently developed mass spectrometry driven proteome analytical approaches specifically targeting the amino (N) terminus of proteins based on the concept of diagonal reverse-phase chromatography. We here review how this so-called combined fractional diagonal chromatography (COFRADIC) technique can be used in combination with differential mass-tagging strategies as to both qualitatively and quantitatively assess protein Nα-acetylation in whole proteomes.

Từ khóa


Tài liệu tham khảo

Polevoda B, Norbeck J, Takakura H, Blomberg A, Sherman F: Identification and specificities of N-terminal acetyltransferases from Saccharomyces cerevisiae. EMBO J. 1999, 18: 6155-6168. 10.1093/emboj/18.21.6155.

Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J: A la carte proteomics with an emphasis on gel-free techniques. Proteomics. 2007, 7: 2698-2718. 10.1002/pmic.200700114.

Kawasaki H, Imajoh S, Suzuki K: Separation of peptides on the basis of the difference in positive charge: simultaneous isolation of C-terminal and blocked N-terminal peptides from tryptic digests. J Biochem (Tokyo). 1987, 102: 393-400.

Taouatas N, Altelaar AF, Drugan MM, Helbig AO, Mohammed S, Heck AJ: SCX-based fractionation of Lys-N generated peptides facilitates the targeted analysis of post-translational modifications. Mol Cell Proteomics. 2008, 8: 190-200. 10.1074/mcp.M800285-MCP200.

Dormeyer W, Mohammed S, Breukelen B, Krijgsveld J, Heck AJ: Targeted analysis of protein termini. J Proteome Res. 2007, 6: 4634-4645. 10.1021/pr070375k.

McDonald L, Robertson DH, Hurst JL, Beynon RJ: Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nat Methods. 2005, 2: 955-957. 10.1038/nmeth811.

Mikami T, Takao T: Selective isolation of N-blocked peptides by isocyanate-coupled resin. Anal Chem. 2007, 79: 7910-7915. 10.1021/ac071294a.

Brown JR, Hartley BS: Location of disulphide bridges by diagonal paper electrophoresis. The disulphide bridges of bovine chymotrypsinogen A. Biochem J. 1966, 101: 214-228.

Gevaert K, Van Damme J, Goethals M, Thomas GR, Hoorelbeke B, Demol H, Martens L, Puype M, Staes A, Vandekerckhove J: Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. Mol Cell Proteomics. 2002, 1: 896-903. 10.1074/mcp.M200061-MCP200.

Gevaert K, Goethals M, Martens L, Van Damme J, Staes A, Thomas GR, Vandekerckhove J: Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol. 2003, 21: 566-569. 10.1038/nbt810.

Staes A, Van Damme P, Helsens K, Demol H, Vandekerckhove J, Gevaert K: Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics. 2008, 8: 1362-1370. 10.1002/pmic.200700950.

Van Damme P, Martens L, Van Damme J, Hugelier K, Staes A, Vandekerckhove J, Gevaert K: Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis. Nat Methods. 2005, 2: 771-777. 10.1038/nmeth792.

Arnesen T, Van Damme P, Polevoda B, Helsens K, Evjenth R, Colaert N, Varhaug JE, Vandekerckhove J, Lillehaug JR, Sherman F, Gevaert K: Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans. Proc Natl Acad Sci USA. 2009, 106: 8157-8162. 10.1073/pnas.0901931106.

Ji J, Chakraborty A, Geng M, Zhang X, Amini A, Bina M, Regnier F: Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. J Chromatogr B Biomed Sci Appl. 2000, 745: 197-210. 10.1016/S0378-4347(00)00192-4.

Dando PM, Fortunato M, Strand GB, Smith TS, Barrett AJ: Pyroglutamyl-peptidase I: cloning, sequencing, and characterisation of the recombinant human enzyme. Protein Expr Purif. 2003, 28: 111-119. 10.1016/S1046-5928(02)00632-0.

Zhang R, Regnier FE: Minimizing resolution of isotopically coded peptides in comparative proteomics. J Proteome Res. 2002, 1: 139-147. 10.1021/pr015516b.

Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M: Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002, 1: 376-386. 10.1074/mcp.M200025-MCP200.

Impens F, Van Damme P, Demol H, Van Damme J, Vandekerckhove J, Gevaert K: Mechanistic insight into taxol-induced cell death. Oncogene. 2008, 27: 4580-4591. 10.1038/onc.2008.96.

Gevaert K, Pinxteren J, Demol H, Hugelier K, Staes A, Van Damme J, Martens L, Vandekerckhove J: Four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells. J Proteome Res. 2006, 5: 1415-1428. 10.1021/pr060026a.

Thông tin
Thông tin xuất bản

BMC Proceedings

Tập 3 Số S6

Thông tin tác giả