Expanding the subproteome of the inner mitochondria using protein separation technologies: One-and two-dimensional liquid chromatography and two-dimensional gel electrophoresis

Molecular and Cellular Proteomics

Volumn 5, Issue 12, 2006, Pages 2392-2411

  McDonald, Todd ^a,d   Sheng, Simon ^a   Stanley, Brian ^a,d   Chen, Dawn ^b   Ko, Young ^c   Cole, Robert N ^b   Pedersen, Peter ^b   Van Eyk, Jennifer E ^a,b,d  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c Johns Hopkins University   (United States)

^d QUEEN S UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; PROTEOME; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DATA BASE; HYDROPHOBICITY; LIQUID CHROMATOGRAPHY; MITOCHONDRIAL MEMBRANE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; RAT; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ANIMALS; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; LIVER; MITOCHONDRIA; MITOCHONDRIAL MEMBRANES; MITOCHONDRIAL PROTEINS; PROTEOME; PROTEOMICS; RATS;

EID: 33845992498     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.T500036-MCP200     Document Type: Article

References (41)

1. Roberts, G.C., and Smith, C. W. (2002) Alternative splicing: combinatorial output from the genome. Curr. Opin. Chem. Biol. 6, 375-383
2. Farriol-Mathis, N., Garavelli, J. S., Boeckmann, B., Duvaud, S., Gasteiger, E., Gateau, A., Veuthey, A.-L., and Bairoch, A. (2004) Annotation of post-translational modifications in the Swiss-Prot knowledge base. Proteomics 4, 1537-1550
3. Van den Bergh, G., and Arckens, L. (2005) Recent advances in 2D electrophoresis: an array of possibilities Expert Rev. Protsomics 2, 243-252
4. Rabilloud, T. (2002) Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 1, 3-10
5. Neverova, I., and Van Eyk, J. E. (2005) Role of chromatographic techniques in proteomic analysis. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 815, 51-63
6. Morris, D. L., Jr., Sutton, J. N., Harper, R. G., and Timperman, A. T. (2204) Reversed-phase HPLC separation of human serum employing a novel saw-tooth gradient: toward multidimensional proteome analysis. J. Proteome Res. 3, 1149-1154
7. Fujii, K., Nakano, T., Hike, H., Usui, F., Bando, Y., Tojo, H., and Nishimura, T. (2004) Fully automated online multi-dimensional protein profiling system for complex mixtures. J. Chromatogr. A 1057, 107-113
8. Garbis, S., Lubec, G., and Fountoulakis, M. (2005) Limitations of current proteomics technologies. J. Chromatogr. A 1077, 1-18
9. Baumann, M., and Meri, S. (2004) Techniques for studying protein heterogeneity and post-translational modifications. Expert Rev. Proteomics 1, 207-217
10. Swanson, S. K., and Washburn, M. P. (2005) The continuing evolution of shotgun proteomics. Drug Discov. Today 10, 719-725
11. Wang, Y., Wu, R., Cho, K. A., Shedden, K. A., Barder, T. J., and Lubman, D. M. (2006) Classification of cancer cell lines using an automated two-dimensional liquid mapping method with hierarchical clustering techniques. Mol. Cell. Proteomics 5, 43-52
12. Sheng, S., Chen, D., and Van Eyk, J. E. (2006) Multi-dimensional liquid chromatography separation of intact proteins by chromatographic focusing and reversed phased of the human serum proteome: optimization and protein database. Mol. Cell. Proteomics 5, 26-34
13. Zheng, S., Schneider, K. A., Barder, T. J., and Lubman, D. M. (2003) Two-dimensional liquid chromatography protein expression mapping for differential proteomic analysis of normal and O157:1-17 Escherichia coli. BioTechniques 35, 1202-1212
14. Lubman, D. M., Kachman, M. T., Wang, H., Gong, S., Yen, F., Hamler, R. L., O'Neil, K. A., Zhu, K., Buchanan, N. S., and Barder, T. J. (2002) Two-dimensional liquid separations-mass mapping of proteins from human cancer cell lysetes. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 782, 183-196
15. Chen, E. I., Hewel, J., Felding-Habermann, B., and Yates, J. R., III (2006) Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT). Mol. Cell. Proteomics 5, 53-6
16. Komatsu, S., Zang, X, and Tanaka, N. (2006) Comparison of two proteomics techniques used to identify proteins regulated by gibberellin in rice. J. Proteome Res. 5, 270-276
17. Gibson, B. W. (2005) The human mitochondrial proteome: oxidative stress, protein modifications and oxidative phosphorylation. Int. J. Biochem. Cell Biol 37, 927-934
18. Pagliarini, D. J., and Dixon, J. E. (2006) Mitochondrial modulation: reversible phosphorylation takes center stage? Trends Biochem. Sci. 31, 26-34
19. Hurd, T. R., Filipovska, A., Costa, N. J., Dahm, C. C., and Murphy, M. P. (2005) Disulphide formation on mitochondrial protein thiols. Biochem. Soc. Trans. 33, 1390-1393
20. Fukada, K., Zhang, F., Vien, A., Cashman, N. R., and Zhu, H. (2004) Mitochondrial proteomic analysis of a cell line model of familial amyotrophic lateral sclerosis. Mol. Cell. Proteomics 12, 1211-1223
21. Taylor, S. W., Fahy, E., Zhang, B., Glenn, G. M., Warnock, D. E., Wiley, S., Murphy, A. N., Gaucher, S. P., Capaldi, R. A., Gibson, B. W., and Ghosh, S. S. (2003) Characterization of the human heart mitochondrial proteome. Nat. Biotechnol. 3, 281-286
22. Gaucher, S. P., Taylor, S. W., Fahy, E., Zhang, B., Warnock, D. E., Ghosh, S. S., and Gibson, B. W. (2004) Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry. J. Proteome Res. 3, 495-505
23. Rezaul, K., Wu, L., Mayya, V., Hwang, S. I., and Han, D. (2005) A systematic characterization of mitochondrial proteome from human T leukemia cells. Mol. Cell. Proteomics 4, 169-181
24. McDonald, T. G., and Van Eyk, J. E. (2003) Mitochondrial proteomics. Undercover in the lipid bilayer. Basic Res. Cardiol. 98, 219-227
25. Taylor, S. W., Fahy, E., and Ghosh, S. S. (2003) Global organellar proteomic. Trends Biotechnol. 21, 82-88
26. Gabaldon, T., and Huynen, M. A. (2004) Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. Biochim. Biophys. Acta 1659, 212-220
27. Santoni, V., Molloy, M., and Rabilloud, T. (2000) Membrane proteins and proteomics: un amour impossible? Electrophoresis 21, 1054-1070
28. Mootha, V. K., Bunkenborg, J., Olsen, J. V., Hjerrid, M., Wisniewski, J. R., Stahl, E., Bolouri, M. S., Ray, H. N., Sihang, S., Kernel, M., Patterson, N., Landers, E. S., and Mann, M. (2003) Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115, 629-640
29. Da Cruz, S., Xenarios, I., Langridge, J., Vilbois, F., Parone, P. A., and Martinou, J. C. (2003) Proteomic analysis of the mouse liver mitochondrial inner membrane. J. Biol. Chem. 278, 41566-41571
30. Da Cruz, S., Parone, P. A., and Martinou, J. C. (2005) Building the mitochondrial proteome. Expert Rev. Proteomics 4, 541-551
31. Calvo, S., Mohit, J., Xie, X., Sheth, S. A., Chang, B., Goldberger, O.A., Spinazzola, A., Zeviani, M., Carr, S. A., and Mootha, V. K. (2006) Systematic identification of human mitochondrial disease genes through integrated genomics. Nat Genet 38, 576-582
32. Pedersen, P. L, Greenawalt, J. W., Reynafarje, B., Hullihen, J., Decker, G. L., Soper, J. W., and Bustamente, E. (1978) Preparation and characterization of mitochondria and submitochondrial particles of rat liver and liver-derived tissues. Methods Cell Biol. 20, 411-481
33. Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68, 850-858
34. Gharahdeghi, F., Weinberg, C. R., Meagher, D. A., Imai, B. S., and Mischa, S. M. (1999) Mass spectrometric identification of proteins from silver-stained polyacrylamide gel: a method for the removal of silver ions to enhance sensitivity. Electrophoresis 20, 601-605
35. Cserzo, M., Wallin, E., Simon, I., von Heijne G., and Elofsson, A. (1997) Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Prot. Eng. 10, 673-676
36. Pirondini, A., Visioli, G., Malcevschi, A., and Marmiroli, N. (2006) A 2-D liquid-phase chromatography for proteomic analysis in plant tissues. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 833, 91-100
37. Linke, T., Ross, A. C., and Harrison, E. H. (2006) Proteomic analysis of rat plasma by two-dimensional liquid chromatography and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J. Chromatogr. A 1123, 160-169
38. Zhu, K., Miller, F. R., Barder, T. J., and Lubman, D. M. (2004) Identification of low molecular weight proteins isolated by 2-D liquid separations. J. Mass Spectrom. 39, 770-778
39. Betgovargez, E., Knudson, V., and Simonian, M. H. (2005) Characterization of proteins in the human serum proteome. J. Biomol. Tech. 16, 306-310
40. Zhu, K., Zhao, J., Lubman, D. M., Miller, F. R., and Barder, T. J. (2005) Protein pl shifts due to posttranslational modifications in the separation and characterization of proteins. Anal. Chem. 77, 2745-2755
41. Clauser, K. R., Baker, P. R., and Burlingame, A. L. (1999) Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871-2882.