New frontiers in proteomics research: A perspective

International Journal of Pharmaceutics

Volumn 299, Issue 1-2, 2005, Pages 1-18

  Dhingra, Vikas ^a   Gupta, Mukta ^a   Andacht, Tracy ^a   Fu, Zhen F ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

Bioinformatics; Mass spectrometry; Post translational modifications; Proteins; Proteomics; Two dimensional electrophoresis

Indexed keywords

CELL PROTEIN; DNA; PROTEIN;

BIOINFORMATICS; CORRELATION ANALYSIS; DISEASE ASSOCIATION; DNA STRUCTURE; GENE FUNCTION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GROWTH CURVE; HUMAN; MASS SPECTROMETRY; MOLECULAR BIOLOGY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; RESEARCH; SAMPLE; SEQUENCE ANALYSIS; SHORT SURVEY; STRUCTURAL PROTEOMICS; STRUCTURE ANALYSIS; TECHNOLOGY; TISSUE; TWO DIMENSIONAL ELECTROPHORESIS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

COMPUTATIONAL BIOLOGY; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; PEPTIDE MAPPING; PROTEIN INTERACTION MAPPING; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 21844453211     PISSN: 03785173     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijpharm.2005.04.010     Document Type: Short Survey

References (98)

1. S. Aldreda, M. Melissa, M.M. Grant, and H.R. Griffiths The use of proteomics for the assessment of clinical samples in research Clin. Biochem. 37 2004 943 952
2. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
3. N.L. Anderson, J. Taylor, A.E. Scandora, B.P. Coulter, and N.G. Anderson The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns Clin. Chem. 27 1981 1807 1820
4. A. Bairoch, and R. Apweiler The SWISS-PROT protein sequence database and its supplement TrEMBL Nucl. Acids Res. 28 2000 45 48
5. Baker, W., vanden Broek, A., Camon, E., Hingamp, P., Sterk, P., Stoesser, G., Tuli, M.A., 2000. The EMBL nucleotide sequence database, Nucl. Acids Res. 28, 19-23.
6. D.A. Benson, I.K. Karsch-Mizrachi, K.D. Lipman, J. Ostell, B.A. Rapp, and D.L. Wheeler GenBank Nucl. Acids Res. 28 2000 15 18
7. K. Berggren, T.H. Steinberg, W.M. Lauber, J.A. Carroll, M.F. Lopez, E. Chernokalskaya, L. Zieske, Z. Diwu, R.P. Haugland, and W.F. Patton A luminescent ruthenium complex for ultra sensitive detection of proteins immobilized on membrane supports Anal. Biochem. 276 1999 129 143
8. B. Bjellqvist, K. Ek, P.G. Righetti, E. Gianazza, A. Gorg, R. Westermeier, and W. Postel Isoelectric focusing in immobilized pH gradients: principle, methodology, and some applications J. Biochem. Biophys. Meth. 6 1982 317 339
9. T.L. Blundel, H. Jhothi, and C. Abell High-throughput crystallography for lead discovery in drug design Nat. Rev. Drug Discov. 1 2002 45 54
10. A. Butt, M.D. Davison, J.A. Young, S.J. Gaskell, S.G. Oliver, and R.J. Benyon Chromatographic sepration as a prelude to two-dimensional electrophoresis in proteomics analysis Proteomics 1 2001 42 53
11. N.V. Bykova, A. Stensballe, H. Egsgaard, O.N. Jensen, and I.M. Moller Phosphorylation of formate dehydrogenase in potato tuber mitochondria J. Biol. Chem. 278 2003 26021 26030
12. L. Carboni, C. Piubelli, P.G. Righetti, B. Jansson, and E. Domenici Proteomic analysis of rat brain tissue: comparison of protocols for two-dimensional gel electrophoresis analysis based on different solubilizing agents Electrophoresis 23 2002 4132 4141
13. J.E. Celis, and P. Gromov 2D electrophoresis: can it be perfected? Curr. Opin. Biotechnol. 10 1999 16 21
14. M. Chevallet, V. Santoni, A. Poinas, D. Rouquie, A. Fuchs, S. Kieffer, M. Rossignol, J. Lunardi, J. Garin, and T. Rabilloud Electrophoresis 19 1998 1901 1909
15. W.W. Cleland Dithiothreitol, a new protective reagent for SH groups Biochemistry 3 1964 480 482
16. G.M. Clore, and A.M. Gronenborn NMR structure determination of proteins and protein complexes larger than 20 kDa Curr. Opin. Chem. Biol. 2 1998 564 570
17. G.S. Cobon, N. Verrills, P. Papakostopoulos, H. Eastwood, and A.W. Linnane The proteomics of ageing Biogerontology 3 2002 133 136
18. L. Coquet, P. Cosette, and T. Jouenne The use of 24 cm, pH 3-11 NL immobiline drystrip gels improves protein separation Life Sci. News 18 2004 12 13
19. C. Damerval, D. DeVienne, M. Zivy, and H. Thiellement Electrophoresis 7 1986 53 54
20. P. Davidsson, L. Paulson, C. Hesse, K. Blennow, and C.L. Nilsson Proteome studies of human cerebrospinal fluid and brain tissue using a preparative two-dimensional electrophoresis approach prior to mass spectrometry Proteomics 1 2001 444 452
21. R.T. Dean, S. Fu, R. Stocker, and M.J. Davies Biochemistry and pathology of radical-mediated protein oxidation J. Biochem. 324 1997 1 18
22. C.L. de Hoog, and M. Mann Proteomics Annu. Rev. Genomics Hum. Genet. 5 2004 267 293
23. C. Denison, A.D. Rudner, S.A. Gerber, C.E. Bakalarski, D. Moazed, and S.P. Gygi A proteomic strategy for gaining insights into protein sumoylation in yeast Mol. Cell Proteomics 4 2005 246 254
24. V. Dhingra, R. Chakrapani, and M.L. Narasu Partial purification of proteins involved in the bioconversion of Arteannuin B to Artemisinin Bioresour. Technol. 73 2000 279 282
25. Dhingra, V., Li, Q., Allison, A.B., Stallknecht, D.E., Fu, Z.F., in press. Proteomic profiling and neurodegeneration in West Nile virus infected neurons. J. Biomed. Biotechnol.
26. M.J. Dunn Gel Electrophoresis of Proteins 1993 BIOS Scientific Publishers Ltd./Alden Press Oxford
27. S. Ficarro, M. McCleland, P. Stukenberg, D. Burke, M. Ross, J. Shabanowitz, D. Hunt, and F. White Phosphoproteaome analysis by mass spectrometry and its application to Saccharomyces cerevisiae Nat. Biotechnol. 20 2002 301 305
28. J.J. Fischer, and O. Jardetzky Nuclear magnetic relaxation study of intermolecular complexes. The mechanism of penicillin binding to serum albumin J. Am. Chem. Soc. 87 1965 3237 3244
29. M. Galvani, L. Rovatti, M. Hamdan, B. Herbert, and P.G. Righetti Protein alkylation in the presence/absence of thiourea in proteome analysis: a matrix assisted laser desorption/ionization-time of flight mass spectrometry investigation Electrophoresis 22 2001 2066 2074
30. M. Galvani, M. Hamdan, B. Herbert, and P.G. Righetti Alkylation kinetics of proteins in preparation of two-dimensional maps: a matrix assisted laser desorption/ionization mass spectrometry investigation Electrophoresis 22 2001 2058 2065
31. J.S. Garavelli The RESID database of protein modifications as a resource and annotation tool Proteomics 4 2004 1527 1533
32. M.B. Goshe, T.P. Conrads, E.A. Panisko, N.H. Angell, T.D. Veenstra, and R.D. Smith Phosphoprotein isotope coded affinity tag approach for isolating and quantitating phosphopeptides in proteome wide analyses Anal. Chem. 74 2001 2578 2586
33. A. Gorg, C. Obermaier, G. Boguth, A. Harder, B. Scheibe, R. Wildgruber, and W. Weiss The current state of two-dimensional electrophoresis with immobilized pH gradients Electrophoresis 21 2000 1037 1053
34. S.G.N. Grant, and W.P. Blackstock Proteomics in neuroscience: from protein to network J. Neurosci. 21 2001 8315 8317
35. M. Gronborg, T.Z. Kristiansen, A. Stensballe, J.S. Andersen, O. Ohara, and M. Mann A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate Mol. Cell Proteomics 1 2002 517 527
36. S.P. Gygi, G.L. Corthals, Y. Zhang, Y. Rochon, and R. Aebersold Evaluation of two-dimensional electrophoresis based proteome analysis technology Proc. Natl. Acad. Sci. U.S.A. 97 2000 9390 9394
37. B.D. Halligan, V. Ruotti, W. Jin, S. Laffoon, S.N. Twigger, and E.A. Dratz ProMoST (protein modification screening tool): a web-based tool for mapping protein modifications on two-dimensional gels Nucl. Acids Res. 1 2004 W638 W644 (Web Server Issue)
38. W. Henzel, T.M. Billeci, J.T. Stults, S.C. Wong, C. Grimley, and C. Watanabe Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases Proc. Natl. Acad. Sci. U.S.A. 90 1993 5011 5015
39. B.R. Herbert, J.C. Sanchez, and L. Bini Two-dimensional electrophoresis: the state of art and future directions M.R. Wilkins K.L. Williams R.D. Appel D.F. Hochstrasser Proteome Research: New Frontiers in Functional Genomics 1997 Springer Berlin 13 33
40. B.R. Herbert, M.P. Molloy, B.A.A. Gooley, J. Walsh, W.G. Bryson, and K.L. Williams Improved protein solubility in two-dimensional electrophoresis using tributyl phosphine as reducing agent Electrophoresis 19 1998 845 851
41. B. Herbert, M. Galvini, M. Hamdan, E. Olivieri, J. MacCarthy, S. Perdson, and P.G. Righetti Reduction and alkylation of proteins in preparation of two-dimensional map analysis: why, when and how? Electrophoresis 22 2001 2046 2057
42. A.L. Hopkins, and C.R. Groom The druggable genome Nat. Rev. Drug Discov. 1 2002 727 730
43. I. Humphrey-Smith, S.J. Cordwell, and W.P. Blackstock Proteome research: complementarily and limitations with respect to the RNA and DNA worlds Electrophoresis 18 1997 1217 1242
44. N. Ibarrola, D.E. Kalume, M. Gronborg, A. Iwahori, and A. Pandey A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture Anal. Chem. 75 2003 6043 6049
45. N. Jamin, and F. Toma NMR studies of protein-DNA interactions Prog. NMR Spectrosc. 38 2001 83 114
46. R.S. Johnson, S.A. Martin, K. Biemann, J.T. Stults, and J.T. Watson Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine Anal. Chem. 59 1987 2621 2625
47. Y. Kimura, Y. Saeki, H. Yokosawa, B. Polevoda, F. Sherman, and H. Hirano N-terminal modifications of the 19S regulatory particle subunits of the yeast proteasome Arch. Biochem. Biophys. 409 2003 341 348
48. S. Kjellstrom, and O.N. Jensen In situ liquid-liquid extraction as a sample preparation method for matrix-assisted laser desorption/ionization MS analysis of polypeptide mixtures Anal. Chem. 75 2003 2362 2369
49. G.V. Kryukov, S. Castellano, S.V. Novoselov, A.V. Lobanov, O. Zehtab, and R. Guigo Characterization of mammalian selenoproteomes Science 300 2003 1439 1443
50. H. Kubinyi Drug research: myths, hype and reality Nat. Rev. Drug Discov. 2 2003 665 668
51. S.A. Lesley, P. Kuhn, A. Godzik, A.M. Daecon, I. Mathews, A. Kreusch, G. Spraggon, and H.E. Klock Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline Proc. Natl. Acad. Sci. U.S.A. 99 2002 11664 11669
52. S. Luche, V. Santoni, and T. Rabilloud Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis Proteomics 3 2003 249 253
53. N.M. Luscombe, D. Greenbaum, and M. Gerstein What is bioinformatics? A proposed definition and overview of the field Meth. Inf. Med. 40 2001 346 358
54. M. Mann, and O.N. Jensen Proteomic analysis of post-translational modifications Nat. Biotechnol. 21 2003 255 261
55. M. Mann, P. Hojrup, and P. Roepstorff Use of mass spectrometric molecular weight information to identify proteins in sequence databases Biol. Mass Spectrosc. 22 1993 338 345
56. T. Marshall, and K.M. Williams Artifacts associated with 2-mercaptoethanol upon high resolution twodimensional electrophoresis Anal. Biochem. 139 1984 502 505
57. D.T. McLachlin, and B.T. Chait Analysis of phosphorylated proteins and peptides by mass spectrometry Curr. Opin. Chem. Biol. 5 2001 591 602
58. M.V. Metodiev, A. Timanova, and D.E. Stone Differential phosphoproteome profiling by affinity capture and tandem matrix-assisted laser desorption/ionization mass spectrometry Proteomics 4 2004 1433 1438
59. A.J. Minn, P.A. Velez, S.L. Schendel, H. Liang, S.W. Muchmore, and S.W. Fesik Bcl-xL forms an ion channel in synthetic lipid membranes Nature 385 1997 353 357
60. H.R. Morris, T. Paxton, M. Panico, R. McDowell, and A. Dell A novel geometry mass spectrometer, the Q-TOF, for low-femtomole/attomole-range biopolymer sequencing J. Prot. Chem. 16 1997 469 479
61. A. Nakamura, and S. Goto Analysis of protein carbonyls with 2,4-dinitrophenyl hydrazine and its antibodies by immunoblot in two dimensional gel electrophoresis J. Biochem. 119 1996 768 774
62. V. Neuhoff, N. Arold, D. Taube, and W. Ehrhardt Improved staining of poteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using coomassie brilliant blue G-250 and R-250 Electrophoresis 9 1988 255 262
63. J.K. Nicholson, and I.D. Wilson High resolution proton magnetic resonance spectroscopy of biological fluids Prog. NMR Spectrosc. 21 1989 444 501
64. Y. Oda, T. Nagasu, and B.T. Chait Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome Nat. Biotechnol. 19 2001 379 382
65. P.H. O'Farrel High resolution two-dimensional electrophoresis of proteins J. Biol. Chem. 250 1975 4007 4021
66. C. Pasquali, I. Fialka, and L.A. Huber Preparative two-dimensional gel electrophoresis of membrane proteins Electrophoresis 18 1997 247 257
67. S.D. Patterson Data analysis - the Achilles heel of proteomics Nat. Biotechnol. 21 2003 221 222
68. W.R. Pearson, and D.J. Lipman Improved tools for biological sequence comparison Proc. Natl. Acad. Sci. U.S.A. 85 1988 2444 2448
69. D.N. Perkins, D.J. Pappin, D.M. Creasy, and J.S. Cottrell Probability based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 1999 3551 3555
70. W. Peti, T. Etezady-Esfarjani, T. Herrmann, H.E. Klock, S.A. Lesley, and K. Wuthrich NMR for structural proteomics of Thermotoga maritima: screening and structure determination J. Struct. Funct. Genomics 5 2004 205 215
71. T. Rabilloud Solubilization of proteins for electrophoretic analysis Electrophoresis 17 1996 813 818
72. T. Rabilloud, E. Gianazza, N. Catto, and P.G. Righetti Amidosulfobetaines, a family of detergents with improved solubilization properties: application for isoelectric focusing under denaturing conditions Anal. Biochem. 185 1990 94 102
73. T. Rabilloud, C. Adessi, A. Giraudel, and J. Lunardi Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients Electrophoresis 18 1997 307 316
74. S. Renfrey, and J. Featherstone Structural proteomics Nat. Rev. Drug Discov. 1 2002 175 176
75. P.G. Righetti, and C.J. Gelfi Immobilized pH gradients for isoelectric focusing. III. Preparative separations in highly diluted gels J. Biochem. Biophys. Meth. 9 1984 103 119
76. P. Roepstorff, and J. Fohlman Proposal for a common nomenclature for sequence ions in mass spectra of peptides Biomed. Mass Spectrom. 11 1984 601 603
77. A.T. Rosengren, J.M. Salmi, T. Aittokallio, J. Westerholm, R. Lahesmaa, T.A. Nyman, and O.S. Nevalainen Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels Proteomics 3 2003 1936 1946
78. A. Shevchenko, M. Wilm, O. Vorm, and M. Mann Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels Anal. Chem. 68 1996 850 858
79. V. Soskic, M. Gorlach, S. Poznanovic, F.D. Boehmer, and J. Godovac-Zimmermann Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor beta receptor Biochemistry 38 1999 1757 1764
80. B.A. Stanley, R.L. Gundry, R.J. Cotter, and J.E. Van Eyk Heart disease, clinical proteomics and mass spectrometry Dis. Markers 20 2004 167 178
81. T. Stasyk, U. Hellman, and S. Souchelnytskyi Life Sci. News 9 2001 9 12
82. D. Staunton, J. Owen, and I.D. Campbell NMR and structural genomics Acc. Chem. Res. 36 2003 207 214
83. T.H. Steinberg, L.J. Jones, R.P. Haugland, and V.L. Singer Sypro orange and sypro red protein gel stains: one step fluorescent staining of denaturing gels for detection of nanogram level protein Anal. Biochem. 239 1996 223 237
84. T.H. Steinberg, B.J. Agnew, K.R. Gee, and W.Y. Leung Global quantitatibe phosphoprotein analysis using multiplex proteomics technology Proteomics 3 2003 1128 1144
85. Y. Tateno, S. Miyazaki, M. Ota, H. Sugawara, and T. Gojobori DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams Nucl. Acids Res. 28 2000 24 26
86. R. Tonge, J. Shaw, B. Middleton, R. Rowlinson, S. Rayner, J. Young, F. Pognan, E. Hawkins, I. Currie, and M. Davison Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology Proteomics 1 2001 377 396
87. M. Unlu, M.E. Morgan, and J.S. Minden Difference gel electrophoresis: a single gel method of detecting changes in protein extracts Electrophoresis 18 1997 2071 2076
88. A.S. Vercoutter-Edouart, X. Czeszak, M. Crepin, J. Lemoine, B. Boilly, X. Le Bourhis, J.P. Peyrat, and H. Hondermarck Proteomic detection of changes in protein synthesis induced by fibroblast growth factor-2 in MCF-7 human breast cancer cells Exp. Cell Res. 262 2001 59 68
89. H. Weissig, and P.E. Bourne An analysis of the Protein Data Bank in search of temporal and global trends Bioinformatics 15 1999 807 831
90. R. Westermeier, and T. Naven Expression proteomics Proteomics in Practice - A Laboratory Manual of Proteome Analysis 2002 Wiley/VCH Germany 11-159
91. M. Wilkins Government backs proteome proposal Nature 378 1995 653
92. M.R. Wilkins, E. Gasteiger, L. Tonella, K. Ou, M. Tyler, J.C. Sanchez, A.A. Gooley, B.J. Walsh, A. Bairoch, R.D. Appel, K.L. Williams, and D.F. Hochstrasser Protein identification with N and C terminal sequence tags in proteome projects J. Mol. Biol. 278 1998 599 608
93. A. Yamagata, D.B. Kristensen, Y. Takeda, Y. Miyamoto, K. Okada, and M. Inamatsu Mapping of phosphorylated proteins on two dimensional polyacrylamide gels using protein phosphatase Proteomics 2 2002 1267 1276
94. A. Yee, X. Chang, A. Pineda-Lucena, B. Wu, A. Semesi, B. Le, T. Ramelot, G.M. Lee, S. Bhattacharyya, P. Gutierrez, A. Denisov, C.H. Lee, J.R. Cort, G. Kozlov, J. Liao, G. Finak, L. Chen, D. Wishart, W. Lee, L.P. McIntosh, K. Gehring, M.A. Kennedy, A.M. Edwards, and C.H. Arrowsmith An NMR approach to structural proteomics Proc. Natl. Acad. Sci. U.S.A. 99 2002 1825 1830
95. W. Ying, Y. Hao, Y. Zhang, W. Peng, E. Qin, and Y. Cai Proteomic analysis on structural proteins of Severe Acute Respiratory Syndrome coronavirus Proteomics 4 2004 492 504
96. J. Zaia Mass spectrometry of oligosaccharides Mass Spectrom. Rev. 23 2004 161 227
97. W. Zhang, and B.T. Chait Profound: an expert system for protein identification using mass spectrometric peptide mapping information Anal. Chem. 72 2000 2482 2488
98. H. Zhou, J.D. Watts, and R. Aebersold A systematic approach to the analysis of protein phosphorylation Nat. Biotechnol. 19 2001 375 378