GOFAST: An integrated approach for efficient and comprehensive membrane proteome analysis

Analytical Chemistry

Volumn 84, Issue 21, 2012, Pages 9008-9014

  Yu, Yanbao ^a   Xie, Ling ^a   Gunawardena, Harsha P ^a   Khatun, Jainab ^b   Maier, Christopher ^a   Spitzer, Wendy ^b   Leerkes, Maarten ^a   Giddings, Morgan C ^a,b   Chen, Xian ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b BOISE STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE SPLICING; ENZYMATIC DIGESTIONS; GENE ONTOLOGY; IDENTIFICATION RATES; INDIVIDUAL PROTEINS; INTEGRATED APPROACH; LARGE-SCALE ANALYSIS; LEUKEMIA CELLS; LIQUID FRACTION; MEMBRANE FRACTION; MEMBRANE PROTEINS; MEMBRANE PROTEOME; MICROWAVE-ASSISTED; PROTEOMICS; SAMPLE PREPARATION; SAMPLE PREPARATION TECHNIQUES;

BIOLOGICAL MEMBRANES; CELL CULTURE; DISEASES; ELECTROPHORESIS; INTEGRATED CONTROL; LOADING; MOLECULAR BIOLOGY; SEPARATION; SOAPS (DETERGENTS); STRESS INTENSITY FACTORS;

PROTEINS;

ISOPROTEIN; MEMBRANE PROTEIN; PROTEOME;

ANALYSIS; ARTICLE; CELL STRAIN K 562; CHEMISTRY; ELECTROPHORESIS; FILTRATION; HUMAN; ISOLATION AND PURIFICATION; METHODOLOGY; PROTEOMICS;

ANALYTIC SAMPLE PREPARATION METHODS; ELECTROPHORESIS; FILTRATION; HUMANS; K562 CELLS; MEMBRANE PROTEINS; PROTEIN ISOFORMS; PROTEOME; PROTEOMICS;

EID: 84868569954     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac300134e     Document Type: Article

References (45)

1. Masuda, T.; Saito, N.; Tomita, M.; Ishihama, Y. Mol. Cell. Proteomics 2009, 8, 2770-2777
2. Tan, S.; Tan, H. T.; Chung, M. C. M. Proteomics 2008, 8, 3924-3932
3. Fischer, F.; Wolters, D.; Rögner, M.; Poetsch, A. Mol. Cell. Proteomics 2006, 5, 444-453
4. Che, F.-Y.; Madrid-Aliste, C.; Burd, B.; Zhang, H.; Nieves, E.; Kim, K.; Fiser, A.; Angeletti, R. H.; Weiss, L. M. Mol. Cell. Proteomics 2011, DOI: 10.1074/mcp.M110.000745.
5. Motoyama, A.; Yates, J. R. Anal. Chem. 2008, 80, 7187-7193
6. Wu, C. C.; Yates, J. R. Nat. Biotechnol. 2003, 21, 262-267
7. Wolff, S.; Otto, A.; Albrecht, D.; Zeng, J. S.; Buttner, K.; Gluckmann, M.; Hecker, M.; Becher, D. Mol. Cell. Proteomics 2006, 5, 1183-1192
8. Zhang, H.; Lin, Q.; Ponnusamy, S.; Kothandaraman, N.; Lim, T. K.; Zhao, C.; Kit, H. S.; Arijit, B.; Rauff, M.; Hew, C.-L.; Chung, M. C. M.; Joshi, S. B.; Choolani, M. Proteomics 2007, 7, 1654-1663
9. Gilmore, J. M.; Washburn, M. P. J. Proteomics 2010, 73, 2078-2091
10. Leth-Larsen, R.; Lund, R. R.; Ditzel, H. J. Mol. Cell. Proteomics 2010, 9, 1369-1382
11. Pasini, E. M.; Kirkegaard, M.; Mortensen, P.; Lutz, H. U.; Thomas, A. W.; Mann, M. Blood 2006, 108, 791-801
12. Yu, Y. B.; Leng, T. H.; Yun, D.; Liu, N.; Yao, J.; Dai, Y.; Yang, P.; Chen, X. Proteomics 2010, 10, 2444-2457
13. Wisniewski, J. R.; Zougman, A.; Nagaraj, N.; Mann, M. Nat. Methods 2009, 6, 359-362
14. Manza, L. L.; Stamer, S. L.; Ham, A. J.; Codreanu, S. G.; Liebler, D. C. Proteomics 2005, 5, 1742-1745
15. Lu, B.; McClatchy, D. B.; Kim, J. Y.; Yates, J. R. Proteomics 2008, 8, 3947-3955
16. Tran, J. C.; Doucette, A. A. Anal. Chem. 2009, 81, 6201-6209
17. Vellaichamy, A.; Tran, J. C.; Catherman, A. D.; Lee, J. E.; Kellie, J. F.; Sweet, S. M. M.; Zamdborg, L.; Thomas, P. M.; Ahlf, D. R.; Durbin, K. R.; Valaskovic, G. A.; Kelleher, N. L. Anal. Chem. 2010, 82, 1234-1244
18. Collier, T. S.; Sarkar, P.; Rao, B.; Muddiman, D. C. J. Am. Soc. Mass Spectrom. 2010, 21, 879-889
19. Botelho, D. M.; Wall, M. J.; Vieira, D. B.; Fitzsimmons, S.; Liu, F.; Doucette, A. A. J. Proteome Res. 2010, 9, 2863-2870
20. Cox, H. D.; Chao, C.-K.; Patel, S. A.; Thompson, C. M. J. Proteome Res. 2008, 7, 570-578
21. Bereman, M. S.; Egertson, J. D.; MacCoss, M. J. Proteomics 2011, 11, 2931-2935
22. Wisniewski, J. R.; Zougman, A.; Mann, M. J. Proteome Res. 2009, 8, 5674-5678
23. Zhou, J.-Y.; Dann, G. P.; Shi, T.; Wang, L.; Gao, X.; Su, D.; Nicora, C. D.; Shukla, A. K.; Moore, R. J.; Liu, T.; Camp, Ii, D. G.; Smith, R. D.; Qian, W.-J. Anal. Chem. 2012, 84, 2862-2867
24. Lill, J. R.; Ingle, E. S.; Liu, P. S.; Pham, V.; Sandoval, W. N. Mass Spectrom. Rev. 2007, 26, 657-671
25. Roesli, C.; Borgia, B.; Schliemann, C.; Gunthert, M.; Wunderli-Allenspach, H.; Giavazzi, R.; Neri, D. Cancer Res. 2009, 69, 5406-5414
26. Ghosh, D.; Beavis, R. C.; Wilkins, J. A. J. Proteome Res. 2008, 7, 1572-1583
27. Ruth, M. C.; Old, W. M.; Emrick, M. A.; Meyer-Arendt, K.; Aveline-Wolf, L. D.; Pierce, K. G.; Mendoza, A. M.; Sevinsky, J. R.; Hamady, M.; Knight, R. D.; Resing, K. A.; Ahn, N. G. J. Proteome Res. 2006, 5, 709-719
28. Wang, Y.; Hancock, W. S.; Weber, G.; Eckerskorn, C.; Palmer-Toy, D. J. Chromatogr., A 2004, 1053, 269-278
29. Cox, B.; Emili, A. Nat. Protoc. 2006, 1, 1872-1878
30. Shevchenko, A.; Tomas, H.; Havlis, J.; Olsen, J. V.; Mann, M. Nat. Protoc. 2007, 1, 2856-2860
31. Huang, D. W.; Sherman, B. T.; Lempicki, R. A. Nat. Protoc. 2008, 4, 44-57
32. Lee, J. E.; Kellie, J. F.; Tran, J. C.; Tipton, J. D.; Catherman, A. D.; Thomas, H. M.; Ahlf, D. R.; Durbin, K. R.; Vellaichamy, A.; Ntai, I.; Marshall, A. G.; Kelleher, N. L. J. Am. Soc. Mass Spectrom. 2009, 20, 2183-2191
33. Krogh, A.; Larsson, B.; von Heijne, G.; Sonnhammer, E. L. L. J. Mol. Biol. 2001, 305, 567-580
34. Gu, S.; Chen, J.; Dobos, K. M.; Bradbury, E. M.; Belisle, J. T.; Chen, X. Mol. Cell. Proteomics 2003, 2, 1284-1296
35. Fagerberg, L.; Jonasson, K.; Heijne, G. v.; Uhlen, M.; Berglund, L. Proteomics 2010, 10, 1141-1149
36. Nagaraj, N.; Wisniewski, J. R.; Geiger, T.; Cox, J.; Kircher, M.; Kelso, J.; Paabo, S.; Mann, M. Mol. Syst. Biol. 2011, 7, 548
37. Reddy, P. M.; Hsu, W.-Y.; Hu, J.-F.; Ho, Y.-P. J. Am. Soc. Mass Spectrom. 2010, 21, 421-424
38. Graveley, B. R. Trends Genet. 2001, 17, 100-107
39. Chang, K.-Y.; Georgianna, D. R.; Heber, S.; Payne, G. A.; Muddiman, D. C. J. Proteome Res. 2010, 9, 1209-1217
40. Tress, M.; Bodenmiller, B.; Aebersold, R.; Valencia, A. Genome Biol. 2008, 9, R162
41. Liu, H.; Sadygov, R. G.; Yates, J. R. Anal. Chem. 2004, 76, 4193-4201
42. Zhang, D. H.; Tai, L. K.; Wong, L. L.; Sethi, S. K.; Koay, E. S. C. Proteomics 2005, 5, 1797-1805
43. Fontana, S.; Alessandro, R.; Barranca, M.; Giordano, M.; Corrado, C.; Zanella-Cleon, I.; Becchi, M.; Kohn, E. C.; De Leo, G. J. Proteome Res. 2007, 6, 4330-4342
44. Nilsson, T.; Mann, M.; Aebersold, R.; Yates, J. R.; Bairoch, A.; Bergeron, J. J. M. Nat. Methods 2010, 7, 681-685
45. Jufvas, A.; Strålfors, P.; Vener, A. V. PLoS One 2011, 6, e15960