Diagonal reverse-phase chromatography applications in peptide-centric proteomics: Ahead of catalogue-omics?

Analytical Biochemistry

Volumn 345, Issue 1, 2005, Pages 18-29

  Gevaert, Kris ^a   Van Damme, Petra ^a   Martens, Lennart ^a   Vandekerckhove, Joël ^a  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROPHORESIS; LIQUID CHROMATOGRAPHY; PROTEOMICS; PULMONARY DISEASES; SOLS;

CHRONIC OBSTRUCTIVE PULMONARY DISEASE; CORE TECHNOLOGY; INTRACELLULAR PROTEINS; PEPTIDE MIXTURES; PHASE SAMPLES; PHOSPHORYLATED PEPTIDES; PURIFIED PROTEIN; REVERSE PHASE CHROMATOGRAPHY;

PEPTIDES;

ALPHA 2 MACROGLOBULIN; BIOLOGICAL MARKER; CELL PROTEIN; CYSTEINE; METHIONINE; PHOSPHOPROTEIN; PROTEOME;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; CHROMATOGRAPHY; CHRONIC OBSTRUCTIVE LUNG DISEASE; COMBINED FRACTIONAL DIAGONAL CHROMATOGRAPHY; CONFERENCE PAPER; HUMAN; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN TARGETING; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; SPUTUM ANALYSIS;

EID: 24144468009     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2005.01.038     Document Type: Conference Paper

References (99)

1. C. Wrotnowski, The future of plasma proteins, Genet. Eng. News 18 (1998) 14.
2. N.L. Anderson, N.G. Anderson, The human plasma proteome: History, character, and diagnostic prospects, Mol. Cell. Proteomics 1 (2002) 845-867.
3. P.H. O'Farrell, High resolution two-dimensional electrophoresis of proteins, J. Biol. Chem. 250 (1975) 4007-4021.
4. J. Klose, Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues: a novel approach to testing for induced point mutations in mammals, Humangenetik 26 (1975) 231-243.
5. B. Bjellqvist, K. Ek, P.G. Righetti, E. Gianazza, A. Gorg, R. Westermeier, W. Postel, Isoelectric focusing in immobilized pH gradients: principle, methodology, and some applications, J. Biochem. Biophys. Meth. 6 (1982) 317-339.
6. P. Madsen, H.H. Rasmussen, H. Leffers, B. Honore, J.E. Celis, Molecular cloning and expression of a novel keratinocyte protein (psoriasis-associated fatty acid-binding protein [PA-FABP]) that is highly up-regulated in psoriatic skin and that shares similarity to fatty acid-binding proteins, J. Invest. Dermatol. 99 (1992) 299-305.
7. S. Borozdenkova, J.A. Westbrook, V. Patel, R. Wait, I. Bolad, M.M. Burke, A.D. Bell, N.R. Banner, M.J. Dunn, M.L. Rose, Use of proteomics to discover novel markers of cardiac allograft rejection, J. Proteome Res. 3 (2004) 282-288.
8. G. Van den Bergh, L. Arckens, Fluorescent two-dimensional difference gel electrophoresis unveils the potential of gel-based proteomics, Curr. Opin. Biotechnol. 15 (2004) 38-43.
9. Y. Hu, X. Huang, G.Y. Chen, S.Q. Yao, Recent advances in gel-based proteome profiling techniques, Mol. Biotechnol. 28 (2004) 63-76.
10. T.H. Steinberg, K. Pretty On Top, K.N. Berggren, C. Kemper, L. Jones, Z. Diwu, R.P. Haugland, Rapid and simple single nanogram detection of glycoproteins in polyacrylamide gels and on electroblots, Proteomics 1 (2001) 841-855.
11. K. Martin, T.H. Steinberg, T. Goodman, B. Schulenberg, J.A. Kilgore, K.R. Gee, J.M. Beechem, W.F. Patton, Strategies and solid-phase formats for the analysis of protein and peptide phosphorylation employing a novel fluorescent phosphorylation sensor dye, Comb. Chem. High Throughput Screen. 6 (2003) 331-339.
12. K. Tanaka, H. Waki, Y. Ido, S. Akita, Y. Yoshida, T. Yoshida, Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry, Rapid Commun. Mass Spectrom. 2 (1988) 151-153.
13. M. Karas, F. Hillenkamp, Laser desorption ionization of proteins with molecular masses exceeding 10,000 Daltons, Anal. Chem. 60 (1998) 2299-2301.
14. J.B. Fenn, M. Mann, C.K. Meng, S.F. Wong, C.M. Whitehouse, Electrospray ionization for mass spectrometry of large biomolecules, Science 246 (1989) 64-71.
15. J.R. Yates, Database searching using mass spectrometry data, Electrophoresis 19 (1998) 893-900.
16. J.E. Shively, The chemistry of protein sequence analysis, EXS 88 (2000)99-117.
17. O.N. Jensen, Modification-specific proteomics: Characterization of post-translational modifications by mass spectrometry, Curr. Opin. Chem. Biol. 8 (2004) 33-41.
18. F.R. Blattner, G. Plunkett III, C.A. Bloch, N.T. Perna, V. Burland, M. Riley, J. Collado-Vides, J.D. Glasner, C.K. Rode, G.F. Mayhew, J. Gregor, N.W. Davis, H.A. Kirkpatrick, M.A. Goeden, D.J. Rose, B. Mau, Y. Shao, The complete genome sequence of Escherichia coli K-12, Science 277 (1997) 1453-1474.
19. A. Goffeau, R. Aert, M.L. Agostini, et al., The yeast genome directory, Nature 387 (Suppl. 5) (1997) 6632.
20. C. elegans sequencing consortium, genome sequence of the nematode C. elegans: a platform for investigating biology, Science 282 (1998) 2012-2018.
21. A. Adams, S.E. Celniker, R.A. Holt, et al., The genome sequence of Drosophila melanogaster, Science 287 (2000) 2185-2195.
22. E.S. Lander, L.M. Linton, B. Birren, et al., Initial sequencing and analysis of the human genome, Nature 409 (2001) 860-921.
23. J.L. Ashurst, J.E. Collins, Gene annotation: prediction and testing, Annu. Rev. Genom. Hum. Genet. 4 (2003) 69-88.
24. J.C. Wiemer, A. Prokudin, Bioinformatics in proteomics: application, terminology, and pitfalls, Pathol. Res. Pract. 200 (2004) 173-178.
25. H. Zhang, W. Yan, R. Aebersold, Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes, Curr. Opin. Chem. Biol. 8 (2004) 66-75.
26. M.R. Wilkins, E. Gasteiger, J.C. Sanchez, A. Bairoch, D.F. Hochstrasser, Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number, Electrophoresis 19 (1998) 1501-1505.
27. V. Santoni, T. Rabilloud, P. Doumas, D. Rouquie, M. Mansion, S. Kieffer, J. Garin, M. Rossignol, Towards the recovery of hydrophobic proteins on two-dimensional electrophoresis gels, Electrophoresis 20 (1999) 705-711.
28. M. Fountoulakis, M.F. Takacs, B. Takacs, Enrichment of low-copy-number gene products by hydrophobic interaction chromatography, J. Chromatogr. A 833 (1999) 157-168.
29. C. Hoogland, K. Mostaguir, J.C. Sanchez, D.F. Hochstrasser, R.D. Appel, Swiss-2DPAGE, ten years later, Proteomics 4 (2004) 2352-2356.
30. M.P. Washburn, D. Wolters, J.R. Yates, Large-scale analysis of the yeast proteome by multidimensional protein identification technology, Nat. Biotechnol. 19 (2001) 242-247.
31. M.J. MacCoss, C.C. Wu, H. Liu, R. Sadygov, J.R. Yates, A correlation algorithm for the automated quantitative analysis of shotgun proteomics data, Anal. Chem. 75 (2003) 6912-6921.
32. C.C. Wu, M.J. MacCoss, K.E. Howell, D.E. Matthews, J.R. Yates, Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis, Anal. Chem. 76 (2004) 4951-4959.
33. H. Liu, R.G. Sadygov, J.R. Yates, A model for random sampling and estimation of relative protein abundance in shotgun proteomics, Anal. Chem. 76 (2004) 4193-4201.
34. E. Durr, J. Yu, K.M. Krasinska, L.A. Carver, J.R. Yates, J.E. Testa, P. Oh, J.E. Schnitzer, Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture, Nat. Biotechnol. 22 (2004) 985-992.
35. S.P. Gygi, B. Rist, S.A. Gerber, F. Turecek, M.H. Gelb, R. Aebersold, Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat. Biotechnol. 17 (1999) 994-999.
36. M.B. Smolka, H. Zhou, S. Purkayastha, R. Aebersold, Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis, Anal. Biochem. 297 (2001) 25-31.
37. S.P. Gygi, B. Rist, T.J. Griffin, J. Eng, R. Aebersold, Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags, J. Proteome Res. 1 (2002) 47-54.
38. 13C-isotope-coded affinity tag and multidimensional chromatography, Mol. Cell. Proteomics 2 (2003) 299-314.
39. H. Lee, E.C. Yi, B. Wen, T.P. Reily, L. Pohl, S. Nelson, R. Aebersold, D.R. Goodlett, Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics, J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 803 (2004) 101-110.
40. C.S. Spahr, S.A. Susin, E.J. Bures, J.H. Robinson, M.T. Davis, M.D. McGinley, G. Kroemer, S.D. Patterson, Simplification of complex peptide mixtures for proteomic analysis: reversible biotinylation of cysteinyl peptides, Electrophoresis 21 (2000) 1635-1650.
41. L. Zhang, Y.L. Guo, H.Q. Liu, A novel class of chemically modified iodo-containing resins: design, synthesis, and application to mass spectrometry-based proteome analysis, J. Mass Spectrom. 39 (2004) 447-457.
42. H. Zhou, J.D. Watts, R. Aebersold, A systematic approach to the analysis of protein phosphorylation, Nat. Biotechnol. 19 (2001) 375-378.
43. Y. Oda, T. Nagasu, B.T. Chait, Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome, Nat. Biotechnol. 19 (2001) 379-382.
44. S. B. Ficarro, M.L. McCleland, P.T. Stukenberg, D.J. Burke, M.M. Ross, J. Shabanowitz, D.F. Hunt, P.M. White, Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae, Nat. Biotechnol. 20 (2002) 301-305.
45. S.A. Beausoleil, M. Jedrychowski, D. Schwartz, J.E. Elias, J. Villen, J. Li, M.A. Cohn, L.C. Cantley, S.P. Gygi, Large-scale characterization of HeLa cell nuclear phosphoproteins, Proc. Natl. Acad. Sci. USA 101 (2004) 12130-12135.
46. B.A. Ballif, J. Villen, S.A. Beausoleil, D. Schwartz, S.P. Gygi, Phosphoproteomic analysis of the developing mouse brain, Mol. Cell. Proteomics 3 (2004) 1093-1101.
47. J. Peng, D. Schwartz, J.E. Elias, C.C. Thoreen, D. Cheng, G. Marsischky, J. Roelofs, D. Finley, S.P. Gygi, A proteomics approach to understanding protein ubiquitination, Nat. Biotechnol. 21 (2003) 921-926.
48. C. Denison, A.D. Rudner, S.A. Gerber, C.E. Bakalarski, D. Moazed, S.P. Gygi, A proteomic strategy for gaining insights into protein sumoylation in yeast, Mol. Cell. Proteomics 4 (2005) 246-254.
49. H. Zhang, X.J. Li, D.B. Martin, R. Aebersold, Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling, and mass spectrometry, Nat. Biotechnol. 21 (2003) 660-666.
50. N. Khidekel, S.B. Ficarro, E.G. Peters, L.C. Hsieh-Wilson, Exploring the O-GlcNAc proteome: direct identification of O-GlcNAc-modified proteins from the brain, Proc. Natl. Acad. Sci. USA 101 (2004) 13132-13137.
51. K. Kuhn, A. Thompson, T. Prinz, J. Muller, C. Baumann, G. Schmidt, T. Neumann, C. Hamon, Isolation of N-terminal protein sequence tags from cyanogen bromide cleaved proteins as a novel approach to investigate hydrophobic proteins, J. Proteome Res. 2 (2003) 598-609.
52. Y. Kho, S.C. Kim, C. Jiang, D. Barma, S.W. Kwon, J. Cheng, J. Jaunbergs, C. Weinbaum, F. Tamanoi, J. Falck, Y. Zhao, A tagging-via-substrate technology for detection and proteomics of farnesylated proteins, Proc. Natl. Acad. Sci. USA 101 (2004) 12479-12484.
53. D. Ren, S. Julka, H.D. Inerowicz, F.E. Regnier, Enrichment of cysteine-containing peptides from tryptic digests using a quaternary amine tag, Anal. Chem. 76 (2004) 4522-4530.
54. T. Liu, W.J. Qian, E.F. Strittmatter, D.G. Camp, G.A. Anderson, B.D. Thrall, R.D. Smith, High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology, Anal. Chem. 76 (2004) 5345-5353.
55. S. Wang, X. Zhang, F.E. Regnier, Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates, J. Chromatogr. A 949 (2002) 153-162.
56. K. Gevaert, J. Vandekerckhove, COFRADIC: the hubble telescope of proteomics, DDT: Targets 3 (2004) S16-S22.
57. J.R. Brown, B.S. Hartley, Location of disulphide bridges by diagonal paper electrophoresis: The disulphide bridges of bovine chymotrypsinogen A, Biochem. J. 101 (1966) 214-228.
58. J. Tang, B.S. Hartley, A diagonal electrophoretic method for selective purification of methionine peptides, Biochem. J. 102 (1967) 593-599.
59. P.J. Butler, J.I. Harris, B.S. Hartley, R. Leberman, Reversible blocking of peptide amino groups by maleic anhydride, Biochem. J. 103 (1967) P78-P79.
60. W.H. Cruickshank, T.M. Radhakrishnan, H. Kaplan, A diagonal paper electrophoretic method for the selective isolation of histidyl peptides, Can. J. Biochem. 49 (1971) 1225-1232.
61. W.H. Cruickshank, B.L. Malchy, H. Kaplan, Diagonal chromatography for the selective purification of tyrosyl peptides, Can. J. Biochem. 52 (1974) 1013-1017.
62. J.L. Cleland, M.F. Powell, S.J. Shire, The development of stable protein formulations: A close look at protein aggregation, deamidation, and oxidation, Crit. Rev. Ther. Drug Carrier Syst. 10 (1993) 307-377.
63. C.W. Sutton, K.S. Pemberton, J.S. Cottrell, J.M. Corbett, C.H. Wheeler, M.J. Dunn, D.J. Pappin, Identification of myocardial proteins from two-dimensional gels by peptide mass fingerprinting, Electrophoresis 16 (1995) 308-316.
64. G. Toennies, R.P. Homiller, The oxidation of amino acids by hydrogen peroxide in formic acid, Am. Chem. Soc. 64 (1942) 3054-3056.
65. C.H.W. Hirs, The oxidation of ribonuclease with performic acid, J. Biol. Chem. 219 (1956) 611-621.
66. K. Gevaert, J. Van Damme, M. Goethals, G.R. Thomas, B. Hoorelbeke, H. Demol, L. Martens, M. Puype, A. Staes, J. Vandekerckhove, Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins, Mol. Cell. Proteomics 1 (2002) 896-903.
67. A. Staes, H. Demol, J. Van Damme, L. Martens, J. Vandekerckhove, K. Gevaert, Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18, J. Proteome Res. 3 (2004) 786-791.
68. D.N. Perkins, D.J. Pappin, D.M. Creasy, J.S. Cottrell, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis 20 (1999) 3551-3567.
69. P. Liu, C.L. Feasley, F.E. Regnier, Optimization of diagonal chromatography for recognizing post-translational modifications, J. Chromatogr. A 1047 (2004) 221-227.
70. K. Gevaert, B. Ghesquiere, A. Staes, L. Martens, J. Van Damme, G.R. Thomas, J. Vandekerckhove, Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies, Proteomics 4 (2004) 897-908.
71. G.L. Ellman, Tissue sulfhydryl groups, Arch. Biochem. Biophys. 82 (1959) 70-77.
72. J.C. Han, G.Y. Han, A procedure for quantitative determination of tris(2-carboxyethyl)phosphine, an odorless reducing agent more stable and effective than dithiothreitol, Anal. Biochem. 220 (1994) 5-10.
73. J.N. Adkins, S.M. Varnum, K.J. Auberry, R.J. Moore, N.H. Angell, R.D. Smith, D.L. Springer, J.G. Pounds, Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry, Mol. Cell. Proteomics 1 (2002) 947-955.
74. R. Pieper, C.L. Gatlin, A.J. Makusky, P.S. Russo, C.R. Schatz, S.S. Miller, Q. Su, A.M. McGrath, M.A. Estock, P.P. Parmar, M. Zhao, S.T. Huang, J. Zhou, F. Wang, R. Esquer-Blasco, N.L. Anderson, J. Taylor, S. Steiner, The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins, Proteomics 3 (2003) 1345-1364.
75. R. Zhang, C.S. Sioma, R.A. Thompson, L. Xiong, F.E. Regnier, Controlling deuterium isotope effects in comparative proteomics, Anal. Chem. 74 (2002) 3662-3669.
76. K. Gevaert, M. Goethals, L. Martens, J. Van Damme, A. Staes, G.R. Thomas, J. Vandekerckhove, Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides, Nat. Biotechnol. 21 (2003) 566-569.
77. J. Vandekerckhove, K. Weber, At least six different actins are expressed in a higher mammal: An analysis based on the amino acid sequence of the amino-terminal tryptic peptide, J. Mol. Biol. 126 (1978) 783-802.
78. T. Okuyama, K. Satake, On the preparation and properties of 2,4,6-trinitrophenyl-amino acids and peptides, J. Biochem. (Tokyo) 47 (1960) 454.
79. R. Fields, The rapid determination of amino groups with TNBS, Methods Enzymol. 25 (1972) 464-468.
80. J.M. Kayembe, R. Louis, J.L. Corhay, T. Bury, R. Agnan, T. Weber, B. Duysinx, M. Radermecker, Usefulness of induced sputum analysis in pulmonary diseases, Acta Clin. Belg. 52 (1997) 106-111.
81. I. Noel-Georis, A. Bernard, P. Falmagne, R. Wattiez, Database of bronchoalveolar lavage fluid proteins, J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 771 (2002) 221-236.
82. Gene ontology consortium, gene ontology: tool for the unification of biology. Nat. Genet. 25 (2000) 25-29.
83. D.F. Schoonbrood, R. Lutter, F.J. Habets, C.M. Roos, H.M. Jansen, T.A. Out, Analysis of plasma-protein leakage and local secretion in sputum from patients with asthma and chronic obstructive pulmonary disease, Am. J. Respir. Crit. Care Med. 150 (1994) 1519-1527.
84. E.J. Oudijk, J.W. Lammers, L. Koenderman, Systemic inflammation in chronic obstructive pulmonary disease, Eur. Respir. J. Suppl. 46 (2003) 85-813.
85. S. Peri, J.D. Navarro, R. Amanchy, et al., Development of human protein reference database as an initial platform for approaching systems biology in humans, Genome Res. 13 (2003) 2363-2371.
86. T. Cawston, S. Carrere, J. Catterall, R. Duggleby, S. Elliott, B. Shingleton, A. Rowan, Matrix metalloproteinases and TIMPs: properties and implications for the treatment of chronic obstructive pulmonary disease, Novartis Found. Symp. 234 (2001) 205-218.
87. M.G. Belvisi, K.M. Bottomley, The role of matrix metalloproteinases (MMPs) in the pathophysiology of chronic obstructive pulmonary disease (COPD): a therapeutic role for inhibitors of MMPs?, Inflamm. Res. 52 (2003) 95-100.
88. S.E. Ong, B. Blagoev, I. Kratchmarova, D.B. Kristensen, H. Steen, A. Pandey, M. Mann, Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Mol. Cell. Proteomics 1 (2002) 376-386.
89. J. Krijgsveld, R.F. Ketting, T. Mahmoudi, J. Johansen, M. Artal-Sanz, C.P. Verrijzer, R.H. Plasterk, A.J. Heck, Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics, Nat. Biotechnol. 21 (2003) 927-931.
90. M. Geng, J. Ji, F.E. Regnier, Signature-peptide approach to detecting proteins in complex mixtures, J. Chromatogr. A 870 (2000) 295-313.
91. M. Munchbach, M. Quadroni, G. Miotto, P. James, Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety, Anal. Chem. 72 (2000) 4047-4057.
92. D.M. Desiderio, M. Kai, Preparation of stable isotope-incorporated peptide internal standards for field desorption mass spectrometry quantification of peptides in biologic tissue, Biomed. Mass Spectrom. 10 (1983) 471-479.
93. P.J. Huber, Robust Statistics, Wiley Interscience, Hoboken, NJ, 1981.
94. D. Lorient, G. Linden, Dephosphorylation of bovine casein by milk alkaline phosphatase, J. Dairy Res. 43 (1976) 19-26.
95. G. Swarup, S. Cohen, D.L. Garbers, Selective dephosphorylation of proteins containing phosphotyrosine by alkaline phosphatases, J. Biol. Chem. 256 (1981) 8197-8201.
96. K. Gevaert, A. Staes, J. Van Damme, S. De Groot, K. Hugelier, H. Demol, L. Martens, M. Goethals, J. Vandekerckhove, Global phosphoproteome analysis on human HepG2 hepatocytes using reverse-phase diagonal liquid chromatography, Proteomics (in press).
97. S.R. Jaffrey, S.H. Snyder, The biotin switch method for the detection of S-nitrosylated proteins, Sci. STKE 86 (2001) PL1.
98. R.J. Mayer, The meteoric rise of regulated intracellular proteolysis, Nat. Rev. Mol. Cell. Biol. 1 (2000) 145-148.
99. R. Frank, R. Hargreaves, Clinical biomarkers in drug discovery and development, Nat. Rev. Drug Discov. 2 (2003) 566-580.