Zooming in: Fractionation strategies in proteomics

Proteomics

Volumn 4, Issue 12, 2004, Pages 3704-3716

  Stasyk, Taras ^a   Huber, Lukas A ^a,b,c,d,e  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^b UNIVERSITY OF INNSBRUCK   (Austria)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^d UNIVERSITY OF GENEVA   (Switzerland)

^e RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

Author keywords

Fractionation; Organelle; Review

Indexed keywords

ANTIBODY; GLYCOPROTEIN; METAL ION; PHOSPHOPEPTIDE; PHOSPHOPROTEIN; REGULATOR PROTEIN;

AFFINITY CHROMATOGRAPHY; AUTOMATION; BINDING AFFINITY; CELL FRACTIONATION; CELL MEMBRANE; CELL ORGANELLE; CELLULAR DISTRIBUTION; EUKARYOTIC CELL; EXTRACTION; GEL PERMEATION CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEIN PHOSPHORYLATION; PROTEIN PURIFICATION; PROTEOMICS; REVIEW; TANDEM MASS SPECTROMETRY; UBIQUITINATION;

ANIMALS; CHROMATOGRAPHY; CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GLYCOPROTEINS; IONS; ISOELECTRIC FOCUSING; MASS SPECTROMETRY; MICE; PEPTIDES; PHOSPHOPROTEINS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; PROTEOME; PROTEOMICS; RATS; SUBCELLULAR FRACTIONS;

EUKARYOTA;

EID: 10644268451     PISSN: 16159853     EISSN: None     Source Type: Journal    
DOI: 10.1002/pmic.200401048     Document Type: Review

References (69)

1. Huber, L. A., Nat. Rev. Mol. Cell. Biol. 2003, 4, 74-80.
2. Dreger, M., Mass Spectrom. Rev. 2003, 22, 27-56.
3. Huber, L. A., Pfaller, K., Vietor, I., Circ. Res. 2003, 92, 962-968.
4. Lee, W. C., Lee, K. H., Anal. Biochem. 2004, 324, 1-10.
5. Lescuyer, P., Hochstrasser, D. F., Sanchez, J. C., Electrophoresis 2004, 25, 1125-1135.
6. Görg, A., Boguth, G., Kopf, A., Reil, G. et al., Proteomics 2002, 2, 1652-1657.
7. Righetti, P. G., Castagna, A., Herbert, B., Reymond, F., Rossier, J. S., Proteomics 2003, 3, 1397-1407.
8. Link, A. J., Trends Biotechnol. 2002, 20, S8-S13.
9. Brunet, S., Thibault, P., Gagnon, E., Kearney, P. et. al., Trends Cell Biol. 2003, 13, 629-638.
10. Taylor, S. W., Fahy, E., Ghosh, S. S., Trends Biotechnol. 2003, 21, 82-88.
11. Warnock, D. E., Fahy, E., Taylor, S. W., Mass Spectrom. Rev. 2004, 23, 259-280.
12. Pasquali, C., Fialka, I., Huber, L. A., J. Chromatogr. B. Biomed. Sci. Appl. 1999, 722, 89-102.
13. Wunderlich, W., Fialka, I., Teis, D., Alpi, A. et al., J. Cell Biol. 2001, 152, 765-776.
14. Teis, D., Wunderlich, W., Huber, L. A., Dev. Cell. 2002, 3, 803-814.
15. Fialka, I., Pasquali, C., Lottspeich, F., Ahorn, H., Huber, L. A., Electrophoresis 1997, 18, 2582-2590.
16. Wu, C. C., MacCoss, M. J., Mardones, G., Finnigan, C. et al., Mol. Biol. Cell. 2004, 15, 2907-2919.
17. Kikuchi, M., Hatano, N., Yokota, S., Shimozawa, N, et al., J. Biol. Chem. 2004, 279, 421-428.
18. Jiang, X. S., Zhou, H., Zhang, L., Sheng, Q. H. et al., Mol. Cell. Proteomics 2004, 3, 441-455.
19. Bauer, A., Kuster, B., Eur. J. Biochem. 2003, 270, 570-578.
20. Ping, P., Circ. Res. 2003, 93, 595-603.
21. Camacho-Carvajal, M. M., Wollscheid, B., Aebersold, R., Steimle, V., Schamel, W. W., Mol. Cell. Proteomics 2004, 3, 176-182.
22. Foster, L. J., De Hoog, C. L., Mann, M., Proc. Natl. Acad. Sci. USA 2003, 100, 5813-5818.
23. Bini, L., Pacini, S., Liberatore, S., Valensin, S. et al., Biochem. J. 2002, 369, 301-309.
24. von Haller, P. D., Donohoe, S., Goodlett, D. R., Aebersold, R., Watts, J. D., Proteomics 2001, 7, 1010-1021.
25. Oliferenko, S., Paiha, K., Harder, T., Gerke, V., J. Cell Biol. 1999, 146, 843-854.
26. Sprenger, R. R., Speijer, D., Back, J. W., De Koster, C. G. et al., Electrophoresis 2004, 25, 156-172.
27. Oh, P., Li, Y., Yu, J., Durr, E. et al., Nature 2004, 429, 629-635.
28. Pasquali, C., Fialka, I., Huber, L. A., Electrophoresis 1997, 18, 2573-2581.
29. Fialka, I., Pasquali, C., Kurzbauer, R., Lottspeich, F., Huber, L. A., Electrophoresis 1999, 20, 331-343.
30. Ramsby, M. L., Makowski, G. S., Methods Mol. Biol. 1999, 112, 53-66.
31. Abdolzade-Bavil, A., Hayes, S., Goretzki, L., Kroger, M. et al., Proteomics 2004, 4, 1397-1405.
32. Ramsby, M. L., Makowski, G. S., Khairallah, E. A., Electrophoresis 1994, 15, 265-277.
33. Elortza, F., Nuhse, T. S., Foster, L. J., Stensballe, A. et al., Mol. Cell. Proteomics 2003, 2, 1261-1270.
34. Salomon, A. R., Ficarro, S. B., Brill, L. M., Brinker, A. et al., Proc. Natl. Acad. Sci. USA 2003, 100, 443-448.
35. Brill, L. M., Salomon, A. R., Ficarro, S. B., Mukherji, M. et al., Anal. Chem. 2004, 76, 2763-2772.
36. Stancato, L. F., Petricoin, E. F. 3rd., Electrophoresis 2001, 22, 2120-2124.
37. Maguire, P. B., Wynne, K. J., Harney, D. F., O'Donoghue, N. M. et al., Proteomics 2002, 2, 642-648.
38. Lim, Y. P., Diong, L. S, Qi, R., Druker, B. J., Epstein, R. J., Mol. Cancer Ther. 2003, 2, 1369-1377.
39. Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R. et al., Proc. Natl. Acad. Sci. USA 2000, 97, 179-184.
40. Steen, H., Kuster, B., Fernandez, M., Pandey, A., Mann, M., J. Biol. Chem. 2002, 277, 1031-1039.
41. Gronborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. S. et al., Mol. Cell. Proteomics 2002, 1, 517-527.
42. Stannard, C., Soskic, V., Godovac-Zimmermann, J., Biochemistry 2003, 42, 13919-13928.
43. Metodiev, M. V., Timanova, A., Stone, D. E., Proteomics 2004, 4, 1433-1438.
44. Shu, H., Chen, S., Bi, Q., Mumby, M., Brekken, D. L., Mol. Cell. Proteomics 2004, 3, 279-286.
45. Andersson, L., Porath, J., Anal. Biochem. 1986, 154, 250-254.
46. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J. et al., Nat. Biotechnol. 2002, 20, 301-305.
47. Feuerstein, I., Morandell, S., Stecher, G., Stasyk, T. et al., Proteomics 2004, in press.
48. Liu, H., Stupak, J., Zheng, J., Keller, B. O. et al., Anal. Chem. 2004, 76, 4223-4232.
49. Nuhse, T. S., Stensballe, A., Jensen, O. N., Peck, S. C., Mol. Cell. Proteomics 2003, 2, 1234-1243.
50. Oda, Y., Nagasu, T., Chait, B. T., Nat. Biotechnol. 2001, 19, 379-382.
51. McLachlin, D. T., Chait, B. T., Anal. Chem. 2003, 75, 6826-6836.
52. Knight, Z. A., Schilling, B., Row, R. H., Kenski, D. M. et al., Nat. Biotechnol. 2003, 21, 1047-1054.
53. Zhou, H., Watts, J. D., Aebersold, R., Nat. Biotechnol. 2001, 19, 375-378.
54. Geng, M., Zhang, X., Bina, M., Regnier, F., J. Chromatogr. B Biomed. Sci. Appl. 2001, 752, 293-306.
55. Ghosh, D., Krokhin, O., Antonovici, M., Ens, W. et al., J. Proteom. Res. 2004, 3, 841-850.
56. Bunkenborg, J., Pilch, B. J., Podtelejnikov, A. V., Wisniewski, J. R., Proteomics 2004, 4, 454-465.
57. Kaji, H., Saito, H., Yamauchi, Y., Shinkawa, T. et al., Nat. Biotechnol. 2003, 21, 667-672.
58. Hitchcock, A. L., Auld, K., Gygi, S. P., Silver, P. A., Proc. Natl. Acad. Sci. USA 2003, 100, 12735-12740.
59. Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C. et al., Nat. Biotechnol. 2003, 21, 921-926.
60. Bae, S. H., Harris, A. G., Hains, P. G., Chen, H. et al., Proteomics 2003, 3, 569-579.
61. Taylor, S. W., Fahy, E., Zhang, B., Glenn, G. M. et al., Nat. Biotechnol. 2003, 21, 281-286.
62. Taylor, S. W., Warnock, D. E., Glenn, G. M., Zhang, B. et al., J. Proteome Res. 2002, 1, 451-458.
63. Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E. et al., Proc. Natl. Acad. Sci. USA 2004, 101, 12130-12135.
64. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E. et al., Nat. Biotechnol. 1999, 17, 676-682.
65. Washburn, M. P., Wolters, D., Yates, J. R. 3rd., Nat. Biotechnol. 2001, 19, 242-247.
66. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., Gygi, S. P., J. Proteome Res. 2003, 2, 43-50.
67. Wienkoop, S., Glinski, M., Tanaka, N., Tolstikov, V., Rapid Commun. Mass Spectrom. 2004, 18, 643-650.
68. Durr, E., Yu, J., Krasinska, K. M., Carver, L. A. et al., Nat. Biotechnol. 2004, 22, 985-992.
69. Gaucher, S. P., Taylor, S. W., Fahy, E., Zhang, B. et al., J. Proteome Res. 2004, 3, 495-505.