Advances in Proteome Analysis by Mass Spectrometry

Abstract

two-dimensional electrophoresis reverse-phase microcapillary liquid chromatography mass spectrometry tandem mass spectrometry electrospray ionization matrix-assisted laser desorption/ionization time-of-flight collision-induced dissociation isotope-coded affinity tag strong cation exchange high performance liquid chromatography The interpretation of the information contained in the genomic sequence of a species with respect to the structure, function, and control of biological processes is a technical and conceptual challenge for current research methods. Systematic and quantitative analysis of gene expression is emerging as a valuable tool to diagnostically distinguish between cell types (1Golub T.R. Slonim D.K. Tamayo P. Huard C. Gaasenbeek M. Mesirov J.P. Coller H. Loh M.L. Downing J.R. Caligiuri M.A. Bloomfield C.D. Lander E.S. Science. 1999; 286: 531-537Crossref PubMed Scopus (9190) Google Scholar, 2Alizadeh A.A. Eisen M.B. Davis R.E. Ma C. Lossos I.S. Rosenwald A. Boldrick J.C. Sabet H. Tran T., Yu, X. Powell J.I. Yang L. Marti G.E. Moore T. Hudson Jr., J. Lu L. Lewis D.B. Tibshirani R. Sherlock G. Chan W.C. Greiner T.C. Weisenburger D.D. Armitage J.O. Warnke R. Staudt L.M. et al.Nature. 2000; 403: 503-511Crossref PubMed Scopus (7996) Google Scholar, 3Scherf U. Ross D.T. Waltham M. Smith L.H. Lee J.K. Tanabe L. Kohn K.W. Reinhold W.C. Myers T.G. Andrews D.T. Scudiero D.A. Eisen M.B. Sausville E.A. Pommier Y. Botstein D. Brown P.O. Weinstein J.N. Nat. Genet. 2000; 24: 236-244Crossref PubMed Scopus (1275) Google Scholar, 4Ross D.T. Scherf U. Eisen M.B. Perou C.M. Rees C. Spellman P. Iyer V. Jeffrey S.S. Van de Rijn M. Waltham M. Pergamenschikov A. Lee J.C. Lashkari D. Shalon D. Myers T.G. Weinstein J.N. Botstein D. Brown P.O. Nat. Genet. 2000; 24: 227-235Crossref PubMed Scopus (1821) Google Scholar, 5Lockhart D.J. Winzeler E.A. Nature. 2000; 405: 827-836Crossref PubMed Scopus (1691) Google Scholar) and to differentiate between states (metabolic, activation, pathological) of a particular cell type (5Lockhart D.J. Winzeler E.A. Nature. 2000; 405: 827-836Crossref PubMed Scopus (1691) Google Scholar, 6Lashkari D.A. DeRisi J.L. McCusker J.H. Namath A.F. Gentile C. Hwang S.Y. Brown P.O. Davis R.W. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 13057-13062Crossref PubMed Scopus (530) Google Scholar, 7Marton M.J. DeRisi J.L. Bennett H.A. Iyer V.R. Meyer M.R. Roberts C.J. Stoughton R. Burchard J. Slade D. Dai H. Bassett Jr., D.E. Hartwell L.H. Brown P.O. Friend S.H. Nat. Med. 1998; 4: 1293-1301Crossref PubMed Scopus (592) Google Scholar). More elaborate strategies such as the combination of systematic, quantitative gene expression analysis with targeted, hypothesis-guided perturbations of cells are being explored for the comprehensive mechanistic analysis of cellular pathways and processes (5Lockhart D.J. Winzeler E.A. Nature. 2000; 405: 827-836Crossref PubMed Scopus (1691) Google Scholar, 7Marton M.J. DeRisi J.L. Bennett H.A. Iyer V.R. Meyer M.R. Roberts C.J. Stoughton R. Burchard J. Slade D. Dai H. Bassett Jr., D.E. Hartwell L.H. Brown P.O. Friend S.H. Nat. Med. 1998; 4: 1293-1301Crossref PubMed Scopus (592) Google Scholar, 8Holstege F.C. Jennings E.G. Wyrick J.J. Lee T.I. Hengartner C.J. Green M.R. Golub T.R. Lander E.S. Young R.A. Cell. 1998; 95: 717-728Abstract Full Text Full Text PDF PubMed Scopus (1595) Google Scholar, 9Roberts C.J. Nelson B. Marton M.J. Stoughton R. Meyer M.R. Bennett H.A. He Y.D. Dai H. Walker W.L. Hughes T.R. Tyers M. Boone C. Friend S.H. Science. 2000; 287: 873-880Crossref PubMed Scopus (719) Google Scholar, 10Ideker T. Thorsson V. Ranish J.A. Christmas R. Buhler J. Eng J.K. Bumgarner R. Goodlett D.R. Aebersold R. Hood L. Science. 2001; 292: 929-934Crossref PubMed Scopus (1649) Google Scholar). Measuring gene expression at the protein level is potentially more informative than the corresponding measurement at the mRNA level. Proteins, the major catalysts of biological function, contain several dimensions of in