Proteomic technologies in modern biomedical science

Biochemistry (Moscow)

Volumn 67, Issue 10, 2002, Pages 1109-1123

  Govorun, V M ^a,b   Archakov, A I ^a  

^a INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^b N N BLOKHIN NATIONAL MEDICAL RESEARCH CENTER OF ONCOLOGY   (Russian Federation)

Author keywords

Biotechnology; Chromatography; Electrophoresis; Protein chip; Proteomics

Indexed keywords

BIOMEDICAL ENGINEERING; BIOTECHNOLOGY; CHROMATOGRAPHIC ANALYSIS; ELECTROPHORESIS; GELS; IMAGE ANALYSIS; MASS SPECTROMETRY;

BIOINFORMATICS;

PROTEINS;

PROTEIN;

BIOLOGY; CHEMISTRY; ISOLATION AND PURIFICATION; MASS SPECTROMETRY; MEDICAL RESEARCH; METABOLISM; METHODOLOGY; PROTEOMICS; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS;

BIOMEDICAL RESEARCH; COMPUTATIONAL BIOLOGY; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; PROTEINS; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 0036817905     PISSN: 00062979     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1020959106412     Document Type: Review

References (99)

1. Wasinger, V.C.,Cordwell, S.J., Cerpa-Poljak, A., Yan, J.X., Gooley, A.A., Wilkins, M.R., Duncan, M.W., Harris, R., Williams, K.L., and Humphery-Smith, I. (1995) Electrophoresis, 16, 1090-1094.
2. Anderson, N.G., and Anderson, L. (1982) Clin. Chem., 28, 739-748.
3. Humphery-Smith, I., Cordwell, S.J., and Blackstock, W.P. (1997) Electrophoresis, 18, 1217-1242.
4. Wilkins, M.R., Williams, K.L., Appel, R.D., and Hochstrasser, D.F. (1997) Proteome Research: New Frontiers in Functional Genomics, Springer, Berlin.
5. Blackstock, W.P., and Weir, M.P. (1999) TIBTECH, 17, 121-127.
6. Service, R.F. (2000) Science, 287, 2136-2138.
7. Champion, K.M., Nishihara, J.C.,Joly, J.C.,and Arnott, D. (2001) Proteomics, 1, 1133-1148.
8. Petersohn, A., Brigulla, M., Haas, S., Hoheisel, J.D., Volker, U., and Hecker, M. (2001) J. Bacteriol., 183, 1517-1531.
9. Buttner, K., Bernhardt, J., Schaff, C., Schmid, R., Mader, U., Eymann, C., Antelmann, H., Volker, A., Volker, U., and Hecker, M. (2001) Electrophoresis, 22, 2908-2935.
10. Tonella, L., Hoogland, C., Binz, P.A., Appel, R.D., Hochstrasser, D.F., and Sanchez, J.C. (2001) Proteomics, 1, 409-423.
11. Anderson, L.N., Matheson, A.D., and Steiner, S. (2000) Curr. Opin. Biotechnol., 11, 408-412.
12. Gygi, S.P., Rochon, Y., Franza, B.R., and Aebersold, R. (1999) Mol. Cello Biol., 19, 1720-1730.
13. Knezevic, V., Leethanakul, C., Bichsel, V.E., Worth, J.M., Prabhu, V.V., Gutkind, J.S., Liotta, L.A., Munson, P.J., Petricoin III, E.F., and Krizman, D.B. (2001) Proteomics, 1, 1271-1278.
14. Adam, B.L., Vlahou, A., Semmes, O.J., and Wright, G.L., Jr. (2001) Proteomics, 1, 1264-1270.
15. Wulfkuhle, J.D., McLean, K.C.,Paweletz, C.P., Sgroi, D.C.,Trock, B.J., Steeg, P.S., and Petricoin III, E.F. (2001) Proteomics, 1, 1205-1215.
16. Emmert-Buck, M.R., Bonner, R.F., Smith, P.D., Chuaqui, R.F., Zhuang, Z., Goldstein, S.R., Weiss, R.A., and Liotta, L.A. (1996) Science, 274, 998-1001.
17. Jones, M.B., Krutzsch, H., Sbu, H., Zhao, Y., Liotta, L.A., Kohn, E.C.,and Petricoin III, E.F. (2002) Proteomics, 2, 76-84.
18. Molloy, M.P. (2000) Analyt. Biochem., 280, 1-10.
19. Herbert, B.R., Molloy, M.P., Gooley, A.A., Walsh, B.J., Bryson, W.G., and Williams, K.L. (1998) Electrophoresis, 19, 845-851.
20. Ruegg, U.T., and Rudinger, J. (1977) Meth. Enzymol., 48, 111-117.
21. MacLaren, J.A. (1971) Text. Res. J., 41, 713.
22. Rabilloud, T., Adessi, C., Giraudel, A., and Lunardi, J. (1997) Electrophoresis, 18, 307-316.
23. Perdew, G.H., Schaup, H.W., and Selivonchick, D.P. (1983) Analyt. Biochem., 135, 453-455.
24. Pasquali, C., Fialka, I., and Huber, L.A. (1997) Electrophoresis, 18, 2573-2581.
25. Santoni, V., Rabilloud, T., Doumas, P., Rouquie, D., Mansion, M., Kieffer, S., Garin, J., and Rossignol, M. (1999) Electrophoresis, 20, 705-711.
26. Molloy, M.P., Herbert, B.R., Slade, M.B., Rabilloud, T., Nouwens, A.S., Williams, K.L., and Gooley, A.A. (2000) Eur. J. Biochem., 267, 2871-2881.
27. Fujiki, Y., Hubbard, A.L., Fowler, S., and Lazarow, P.B. (1982) J. Cell, Biol., 93, 97-102.
28. Kamo, M., Kawakami, T., Miyatake, N., and Tsugita, A. (1995) Electrophoresis, 76, 423-430.
29. Garrels, J.I., Me Laughlin, C.S., Warner, J.Ft., Futcher, B., Latter, G.I., Kobayashi, R., Schwender, B., Voipe, T., Anderson, D.S., Mesquita-Fuentes, R., and Payne, W.E. (1997) Electrophoresis, 18, 1347-1360.
30. Perrot, M., Sagliocco, F., Mini, T., Monribot, C., Schneider, U., Shevchenko, A., Mann, M., Jeno, P., and Boucherie, H. (1999) Electrophoresis, 20, 2280-2298.
31. Costa, P., Pionneau, C., Bauw, G., Dubos, C., Bahrmann, N., Kremer, A., Frigerio, J.M., and Plomion, C. (1999) Electrophoresis, 20, 1098-1108.
32. Santoni, V., Rouquie, D., Doumas, P., Mansion, M., Boutry, M., Degand, H., Dupree, P., Packman, L., Sherrier, J., Prime, T., Bauw, G., Posada, E., Rouze, P., Dehais, P., Sahnoun, I., Barlier, I., and Rossignol, M. (1998) Plant, J., 16, 633-641.
33. Link, A.J., Eng, J., Schieltz, D.M., Carmack, E., Mize, G.J., Morris, D.R., Garvik, B.M., and Yates III, J.R. (1999) Nat. Biotechnol., 17, 676-682.
34. Mirgorodskaya, O.A., Kozmin, Y.P., Titov, M.I., Korner, R., Sonksen, C.P., and Roepstorff, P. (2000) Rapid Commun. Mass Spectrom., 14, 1226-1232.
35. O'Farrell, P.H. (1975) J. Biol. Chem., 250, 4007-4021.
36. Link, A.J. (1999) 2-D Proteome Analysis Protocols, Humana Press, Totova, New Jersey.
37. Anderson, N.G., and Anderson, N.L. (1978) Analyt. Biochem., 85, 331-354.
38. Dunn, M.J. (1993) Gel Electrophoresis of Proteins, BIOS Scientific Publishers Ltd. Alden Press, Oxford.
39. Giörg, A., Postel, W., Westermeier, R., Gianazza, E., and Righetti, P.G. (1980) J. Biochem. Biophys. Meth., 3, 273-284.
40. Görg, A., Postel, W., and Günther, S. (1988) Electrophoresis, 9, 531-546.
41. Görg, A., Postel, W., Friedrich, C., Kuick, R., Strahler, J.R., and Hanash, S.M. (1991) Electrophoresis, 12, 653-658.
42. Laemmli, U.K. (1970) Nature, 227, 680-685.
43. Bjellqvist, B., Ek, K., Righetti, P.G., Gianazza, E., Görg, A., Westermeier, R., and Postel, W. (1982) J. Biochem. Biophys. Meth., 6, 317-339.
44. Görg, A. (1993) Biochem. Soc. Trans., 21, 130-132.
45. Matsui, N.M., Smith-Beckerman, D.M., Fichmann, J., and Epstein, L.B. (1999) in 2-D Proteome Analysis Protocols, Humana Press, Totova, New Jersey, p. 211.
46. Futcher, B., Latter, G.I., Monardo, P., McLaughlin, C.S., and Garrets, J.I. (1999) Mol. Cell. Biol., 19, 7357-7368.
47. Gygi, S.P., Corthals, G.L., Zhang, Y., Rochon, Y., and Aebersold, R. (2000) Proc. Natl. Acad. Sci. USA, 15, 9390-9395.
48. Herbert, B.R., and Righetti, P.G. (2000) Electrophoresis, 21, 3639-3648.
49. Herbert, B.R., Harry, J.L., Packer, N.H., Gooley, A.A., Pedersen, S.K., and Williams, K.L. (2001) Trends BiotechnoL, 19 (Suppl.), s3-s9.
50. Nesterenko, M.V., Tilley, M., and Upton, S.J. (1994) J. Biochem. Biophys. Meth., 28, 239-242.
51. Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Analyt. Chem., 68, 850-858.
52. Neuhoff, V., Arold, N., Taube, D., and Ehrhardt, W. (1988) Electrophoresis, 9, 255-262.
53. Yan, J.X., Harry, R.A., Spibey, C., and Dunn, M.J. (2000) Electrophoresis, 21, 3657-3665.
54. Bilban, M., Buehler, L.K., Head, S., Desoye, G., and Quaranta, V. (2002) Curr. Issues Mol, Biol., 4, 57-64.
55. Westermeier, R. (2001) in Proc. Proteomic Forum 2001, Technische Universitat Muenchen, Germany, p. 53.
56. Yates III, J.R., Link, A.J., and Schieltz, D. (2000) Meth. Mol, Biol., 146, 17-26.
57. Washburn, M.P., Wolters, D., and Yates III, J.R. (2001) Nat. Biotechnol., 19, 242-247.
58. Gevaert, K., and Vandekerckhove, J. (2000) Electrophoresis, 21, 1145-1154.
59. Wolters, D.A., Washburn, M.P., and Yates III, J.R. (2001) Analyt. Chem., 73, 5683-5690.
60. Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H., and Aebersold, R. (1999) Nat. Biotechnol., 17, 994-999.
61. Moseley, M.A. (2001) Trends Biotechnol., 19 (Suppl.), s10-s16.
62. Aebersold, R., and Goodlett, D.R. (2001) Chem. Rev., 101, 269-295.
63. Nordhoff, E., Egelhofer, V., Giavalisco, P., Eickhoff, H., Horn, M., Przewieslik, T., Theiss, D., Schneider, U., Lehrach, H., and Gobom, J. (2001) Electrophoresis, 22, 2844-2855.
64. Roepstorff, P. (2000) EXS, 88, 81-97.
65. Gygi, S.P., and Aebersold, R. (2000) in Using Mass-Spectrometry for Quantitative Proteomics. Proteomics: A Trends Guide, pp. 31-36.
66. Andersen, J.S., and Mann, M. (2000) FEBS Lett., 480, 25-31.
67. Kussmann, M., and Roepstorff, P. (2000) Meth. Mol. Biol., 146, 405-424.
68. Chaurand, P., Luetzenkirchen, F., and Spengler, B. (1999) J. Am. Soc. Mass Spectrom., 10, 91-103.
69. Spengler, B. (1997) J. Mass Spectrom., 32, 1019-1036.
70. Jonscher, K.R., and Yates III, J.R. (1997) Analyt. Biochem., 244, 1-15.
71. Qin, J., and Chait, B.T. (1997) Analyt. Chem., 69, 4002-4009.
72. Wilm, M., and Mann, M. (1996) Analyt. Chem., 68, 1-8.
73. Papayannopoulos, I.A. (1995) Mass Spectrom. Rev., 14, 49-73.
74. Hillenkamp, F., Karas, M., Beavis, R.C.,and Chait, B.T. (1991) Analyt. Chem., 63, 1193A-1203A.
75. Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F., and Whitehouse, C.M. (1990) Mass Spectrom. Rev., 9, 37-70.
76. Twerenbold, D., Gerber, D., Gritti, D., Gonin, I., Netuschill, A., Rossel, F., Schenker, D., and Vuilleumier, J.-L. (2001) Proteomics, 1, 66-69.
77. Wright, G.L., Cazares, L.H., Leung, S.M., Nasim, S., Adam, B., Yip, T., Schellhammer, P.F., Gong, L., and Vlahou, A. (1999) Prost. Cancer Prost. Dis., 2, 264-276.
78. Vlahou, A., Schellhammer, P.F., Mendrinos, S., Patel, K., Kondylis, F.I., Gong, L., Nasim, S., and Wright, G.L., Jr. (2001) Am. J. Pathol., 158, 1491-1502.
79. He, M., and Taussig, M.J. (2001) Nucleic Acids Res., 29, e73.
80. Cahill, D.J. (2001) J. Immunol. Meth., 250, 81-91.
81. Bolon, P. (2002) in Protein and Peptide Arrays: Pitfalls, Prospects, and Promise, 26-27 March, Munich, Germany.
82. Rain, J.-C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schaechter, V., Chemama, Y., Labigne, A., and Legrain, P. (2001) Nature, 409, 211-215.
83. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J.M. (2000) Nature, 403, 623-627.
84. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001) Proc. Natl. Acad. Sci. USA, 98, 4569-4574.
85. Natsume, T., Nakayama, H., and Isobe, T. (2001) Trends Biotechnol., 19 (Suppl.), s28-s33.
86. Malmqvist, M., and Karlsson, R. (1997) Curr. Opin. Chem. Biol., 1, 378-383.
87. Szabo, A., Stolz, L., and Granzow, R. (1995) Curr. Opin. Struct. Biol., 5, 699-705.
88. Appel, R.D., Bairoch, A., Sanchez, J.C.,Vargas, J.R., Golaz, O., Pasquali, C., and Hochstrasser, D.F. (1996) Electrophoresis, 17, 540-546.
89. Lemkin, P.F. (1997) Electrophoresis, 18, 2759-2773.
90. Pleissner, K.P., Oswald, H., and Wegner, S. (2001) in Proteomics. From Protein Sequence to Function (Pennington, R., and Dunn, M.J., eds.) BIOS Scientific Publishers, Oxford, pp. 131-149.
91. Appel, R.D., Vargas, J.R., Palagi, P.M., Walther, D., and Hochstrasser, D.F. (1997) Electrophoresis, 18, 2735-2748.
92. Smilansky, Z. (2001) Electrophoresis, 22, 1616-1626.
93. Veeser, S., Dunn, M.J., and Yang G.-Z. (2001) Proteomics, 1, 856-870.
94. Wilkins, M.R., Gasteiger, E., Wheeler, C., Lindskog, I., Sanchez, J.-C., Bairoch, A., Appel, R.D., Dunn, M.D., and Hochstrasser, D.F. (1998) Electrophoresis, 19, 3199-3206.
95. Pappin, D.J.C., Hojrup, P., and Bleasby, A.J. (1993) Curr. Biol., 3, 327-332.
96. Perkins, D.N., Pappin, D.J.C., Creasy, D.M., and Cottrell, J.S. (1999) Electrophoresis, 20, 3551-3567.
97. Zhang, W., and Chait, B.T. (2000) Analyt. Chem., 72, 2482-2489.
98. Taylor, J.A., Walsh, K.A., and Johnson, R.S. (1996) Rapid Commun. Mass Spectrom., 10, 679-687.
99. Green, D.M., and Swets, J.A. (1966) in Signal Detection Theory and Psychophysics, Wiley, Reprinted 1974 by Krieger, Huntington, New York.