Advances in Proteome Analysis by Mass Spectrometry

Journal of Biological Chemistry

Volumn 276, Issue 49, 2001, Pages 45497-45500

  Griffin, Timothy J ^a   Aebersold, Ruedi ^b  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; CHEMICAL LABELING; INSTRUMENTATION; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; SHORT SURVEY; TANDEM MASS SPECTROMETRY; TECHNOLOGY; TWO DIMENSIONAL GEL ELECTROPHORESIS; CHEMISTRY; METHODOLOGY; REVIEW;

PROTEOME;

PROTEOME; SPECTRUM ANALYSIS, MASS; SUPPORT, NON-U.S. GOV'T; SUPPORT, U.S. GOV'T, P.H.S.;

EID: 0035824631     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.R100014200     Document Type: Short Survey

References (78)

1. Golub, 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., and Lander, E. S. (1999) Science 286, 531-537
2. Alizadeh, 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, J., Jr., 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. (2000) Nature 403, 503-511
3. Scherf, 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., and Weinstein, J. N. (2000) Nat. Genet. 24, 236-244
4. Ross, 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., and Brown, P. O. (2000) Nat. Genet. 24, 227-235
5. Lockhart, D. J., and Winzeler, E. A. (2000) Nature 405, 827-836
6. Lashkari, D. A., DeRisi, J. L., McCusker, J. H., Namath, A. F., Gentile, C., Hwang, S. Y., Brown, P. O., and Davis, R. W. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 13057-13062
7. Marton, 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, D. E., Jr., Hartwell, L. H., Brown, P. O., and Friend, S. H. (1998) Nat. Med. 4, 1293-1301
8. Holstege, F. C., Jennings, E. G., Wyrick, J. J., Lee, T. I., Hengartner, C. J., Green, M. R., Golub, T. R., Lander, E. S., and Young, R. A. (1998) Cell 95, 717-728
9. Roberts, 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., and Friend, S. H. (2000) Science 287, 873-880
10. Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., and Hood, L. (2001) Science 292, 929-934
11. O'Farrell, P. H. (1975) J. Biol. Chem. 250, 4007-4021
12. Klose, J. (1975) Humangenetik 26, 231-243
13. Karas, M., and Hillenkamp, F. (1988) Anal. Chem. 60, 2299-2301
14. Hillenkamp, F., Karas, M., Beavis, R. C., and Chait, B. T. (1991) Anal. Chem. 63, 1193A-1203A
15. Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., and Whitehouse, C. M. (1989) Science 246, 64-71
16. Banks, J. F., Jr., and Whitehouse, C. M. (1996) Methods Enzymol. 270, 486-519
17. Aebersold, R. H., Leavitt, J., Saavedra, R. A., Hood, L. E., and Kent, S. B. (1987) Proc. Natl. Acad. Sci. U. S. A. 84, 6970-6974
18. Lin, C. S., Aebersold, R. H., Kent, S. B., Varma, M., and Leavitt, J. (1988) Mol. Cell. Biol. 8, 4659-4668
19. Humphery-Smith, I., Cordwell, S. J., and Blackstock, W. P. (1997) Electrophoresis 18, 1217-1242
20. Dunn, M. J., and Corbett, J. M. (1996) Methods Enzymol. 271, 177-203
21. Shevchenko, A., Jensen, O. N., Podtelejnikov, A. V., Sagliocco, F., Wilm, M., Vorm, O., Mortensen, P., Boucherie, H., and Mann, M. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 14440-14445
22. Clauser, K. R., Hall, S. C., Smith, D. M., Webb, J. W., Andrews, L. E., Tran, H. M., Epstein, L. B., and Burlingame, A. L. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 5072-5076
23. Pandey, A., and Mann, M. (2000) Nature 405, 837-846
24. Patterson, S. D., and Aebersold, R. (1995) Electrophoresis 16, 1791-1814
25. Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Anal. Chem. 68, 850-858
26. Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C., Grimley, C., and Watanabe, C. (1993) Proc. Natl. Acad. Sci. U. S. A. 90, 5011-5015
27. Wilm, M., Shevchenko, A., Houthaeve, T., Breit, S., Schweigerer, L., Fotsis, T., and Mann, M. (1996) Nature 379, 466-469
28. Wilm, M., and Mann, M. (1996) Anal. Chem. 68, 1-8
29. Shabanowitz, J., Settlage, R. E., Marto, J. A., Christian, R. E., White, F. M., Russo, P. S., Martin, S. E., and Hunt, D. F. (2000) in Mass Spectrometry in Biology and Medicine (Burlingame, A. L., Carr, S. A., and Baldwin, M. A., eds) pp, 163-177, Humana Press, Totowa, NJ
30. Hunt, D. F., Henderson, R. A., Shabanowitz, J., Sakaguchi, K., Michel, H., Sevilir, N., Cox, A. L., Appella, E., and Engelhard, V. H. (1992) Science 255, 1261-1263
31. McCormack, A. L., Schieltz, D. M., Goode, B., Yang, S., Barnes, G., Drubin, D., and Yates, J. R., III (1997) Anal. Chem. 69, 767-776
32. Davis, M. T., Stahl, D. C., Hefta, S. A., and Lee, T. D. (1995) Anal. Chem. 67, 4549-4556
33. Ducret, A., Van Oostveen, I., Eng, J. K., Yates, J. R., III, and Aebersold, R. (1998) Protein Sci. 7, 706-719
34. Haynes, P. A., Fripp, N., and Aebersold, R. (1998) Electrophoresis 19, 939-945
35. Gatlin, C. L., Eng, J. K., Cross, S. T., Detter, J. C., and Yates, J. R., III (2000) Anal. Chem. 72, 757-763
36. Figeys, D., and Aebersold, R. (1997) Electrophoresis 18, 360-368
37. Courchesne, P. L., Jones, M. D., Robinson, J. H., Spahr, C. S., McCracken, S., Bentley, D. L., Luethy, R., and Patterson, S. D. (1998) Electrophoresis 19, 956-967
38. Hunt, D. F., Yates, J. R., III, Shabanowitz, J., Winston, S., and Hauer, C. R. (1986) Proc. Natl. Acad. Sci. U. S. A. 83, 6233-6237
39. Papayannopoupos, I. A. (1995) Mass Spectrom. Rev. 14, 49-73
40. Beavis, R. C., and Fenyo, D. (2000) in Proteomics: a Trends Guide (Mann, M., and Blackstock, W., eds) pp. 22-27, Elsevier, London
41. Eng, J., McCormack, A. L., and Yates, J. R., III (1994) J. Am. Soc. Mass Spectrom. 5, 976-989
42. Blackstock, W. (2000) in Proteomics: a Trends Guide (Mann, M., and Blackstock, W., eds) pp. 12-17, Elsevier, London
43. Yates, J. R., III (2000) Trends Genet. 16, 5-8
44. Gygi, S. P., Corthals, G. L., Zhang, Y., Rochon, Y., and Aebersold, R. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 9390-9395
45. Rabilloud, T., Adessi, C., Giraudel, A., and Lunardi, J. (1997) Electrophoresis 18, 307-316
46. Gorg, A., Obermaier, C., Boguth, G., Harder, A., Scheibe, B., Wildgruber, R., and Weiss, W. (2000) Electrophoresis 21, 1037-1053
47. Corthals, G. L., Molloy, M. P., Herbert, B. R., Williams, K. L., and Gooley, A. A. (1997) Electrophoresis 18, 317-323
48. Steinberg, T. H., Chernokalskaya, E., Berggren, K., Lopez, M. F., Diwu, Z., Haugland, R. P., and Patton, W. F. (2000) Electrophoresis 21, 486-496
49. Wildgruber, R., Harder, A., Obermaier, C., Boguth, G., Weiss, W., Fey, S. J., Larsen, P. M., and Gorg, A. (2000) Electrophoresis 21, 2610-2616
50. Lopez, M. F. (2000) Electrophoresis 21, 1082-1093
51. De Leenheer, A. P., and Thienpont, L. M. (1992) Mass Spectrom. Rev. 11, 249-307
52. Kenyon, G. L., and Bruice, T. W. (1977) Methods Enzymol. 47, 407-430
53. Sechi, S., and Chait, B. T. (1998) Anal. Chem. 70, 5150-5158
54. Fenyo, D., Qin, J., and Chait, B. T. (1998) Electrophoresis 19, 998-1005
55. Spahr, C. S., Susin, S. A., Bures, E. J., Robinson, J. H., Davis, M. T., McGinley, M. D., Kroemer, G., and Patterson, S. D. (2000) Electrophoresis 21, 1635-1650
56. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Nat. Biotechnol. 17, 994-999
57. Munchbach, M., Quadroni, M., Miotto, G., and James, P. (2000) Anal. Chem. 72, 4047-4057
58. Ji, J., Chakraborty, A., Geng, M., Zhang, X., Amini, A., Bina, M., and Regnier, F. (2000) J. Chromatogr. B Biomed. Appl. 745, 197-210
59. Oda, Y., Huang, K., Cross, F. R., Cowburn, D., and Chait, B. T. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 6591-6596
60. Pasa-Tolie, L., Jensen, P., Anderson, G., Lipton, M., Peden, K., Martinovic, S., Tolic, N., Bruce, J., and Smith, R. (1999) J. Am. Chem. Soc. 121, 7949-7950
61. Washburn, M. P., and Yates, J. R. (2000) in Proteomics: a Trends Guide (Mann, M., and Blackstock, W., eds) pp. 27-30, Elsevier, London
62. Opiteck, G. J., Lewis, K. C., Jorgenson, J. W., and Anderegg, R. J. (1997) Anal. Chem. 69, 1518-1524
63. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., and Yates, J. R., 3rd. (1999) Nat. Biotechnol. 17, 676-682
64. Washburn, M. P., Wolters, D., and Yates, J. R., III (2001) Nat. Biotechnol. 19, 242-247
65. Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001) Nat. Biotechnol. 19, 946-951
66. Zhou, H., Watts, J. D., and Aebersold, R. (2001) Nat. Biotechnol. 19, 375-378
67. Liu, Y., Patricelli, M. P., and Cravatt, B. F. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 14694-14699
68. Patricelli, M. P., Lovato, M. A., and Cravatt, B. F. (1999) Biochemistry 38, 9804-9812
69. Greenbaum, D., Medzihradszky, K. F., Burlingame, A., and Bogyo, M. (2000) Chem. Biol. 7, 569-581
70. Cravatt, B. F., and Sorensen, E. J. (2000) Curr. Opin. Chem. Biol. 4, 663-668
71. Loboda, A. V., Krutchinsky, A. N., Bromirski, M., Ens, W., and Standing, K. G. (2000) Rapid Commun. Mass Spectrom. 14, 1047-1057
72. Shevchenko, A., Loboda, A., Shevchenko, A., Ens, W., and Standing, K. G. (2000) Anal. Chem. 72, 2132-2141
73. Griffin, T. J., Loboda, A., Gygi, S. P., Rist, B., Jilkine, A., Ens, W., Standing, K. G., and Aebersold, R. (2001) Anal. Chem. 73, 978-986
74. Medzihradszky, K. F., Campbell, J. M., Baldwin, M. A., Falick, A. M., Juhasz, P., Vestal, M. L., and Burlingame, A. L. (2000) Anal. Chem. 72, 552-558
75. Martin, S. E., Shabanowitz, J., Hunt, D. F., and Marto, J. A. (2000) Anal. Chem. 72, 4266-4274
76. Bruce, J. E., Anderson, G. A., Wen, J., Harkewiez, R., and Smith, R. D. (1999) Anal. Chem. 71, 2595-2599
77. Goodlett, D. R., Bruce, J. E., Anderson, G. A., Rist, B., Pasa-Tolic, L., Fiehn, O., Smith, R. D., and Aebersold, R. (2000) Anal. Chem. 72, 1112-1118
78. Conrads, T. P., Anderson, G. A., Veenstra, T. D., Pasa-Tolie, L., and Smith, R. D. (2000) Anal. Chem. 72, 3349-3354