Proteomic analysis of lipid-protein complexes

Journal of Lipid Research

Volumn 50, Issue 5, 2009, Pages 781-786

  Vaisar, Tomas ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Integral membrane proteins; Lipoproteins; Mass spectrometry

Indexed keywords

LIPID; LIPOPROTEIN; MEMBRANE PROTEIN; PEPTIDE; PROTEIN;

ANALYTIC METHOD; COMPLEX FORMATION; HUMAN; HYDROPHOBICITY; LIPID ANALYSIS; LIPOPROTEIN BLOOD LEVEL; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN ISOLATION; PROTEOMICS; REVIEW; SOLUBILIZATION; TANDEM MASS SPECTROMETRY; ISOLATION AND PURIFICATION; SOLUBILITY;

LIPIDS; PROTEINS; PROTEOMICS; SOLUBILITY;

EID: 67649713420     PISSN: 00222275     EISSN: 15397262     Source Type: Journal    
DOI: 10.1194/jlr.R900005-JLR200     Document Type: Review

References (73)

1. Fenn, J. B., M. Mann, C. K. Meng, S. F. Wong, and C. M. Whitehouse. 1989. Electrospray ionization for mass spectrometry of large biomolecules. Science. 246: 64-71.
2. Tanaka, K. 2003. The Origin of Macromolecule Ionization by Laser Irradiation (Nobel Lecture)13. Angew.Chem. Int. Ed. Engl. 42: 3860-3870.
3. McLafferty, F. W., K. Breuker, M. Jin, X. Han, G. Infusini, H. Jiang, X. Kong, and T. P. Begley. 2007. Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J. 274: 6256-6268.
4. Aebersold, R., and M. Mann. 2003. Mass spectrometry-based proteomics. Nature. 422: 198-207.
5. Motoyama, A., and J. R. Yates III. 2008. Multidimensional LC separations in shotgun proteomics. Anal. Chem. 80: 7187-7193.
6. Saito, H., S. Lund-Katz, and M. C. Phillips. 2004. Contributions of domain structure and lipid interaction to the functionality of exchangeable human apolipoproteins. Prog. Lipid Res. 43: 350-380.
7. Silva, R. A. G. D., L. A. Schneeweis, S. C. Krishnan, X. Zhang, P. H. Axelsen, and W. S. Davidson. 2007. The structure of apolipoprotein A-II in discoidal high density lipoproteins. J. Biol. Chem. 282: 9713-9721.
8. Tubb, M. R., R. A. G. D. Silva, J. Fang, P. Tso, and W. S. Davidson. 2008. A three-dimensional homology model of lipid-free apolipoprotein A-IV using cross-linking and mass spectrometry. J. Biol. Chem. 283: 17314-17323.
9. Thomas, M. J., S. Bhat, and M. G. Sorci-Thomas. 2008. Three-dimensional models of HDL apoA-I: implications for its assembly and function. J. Lipid Res. 49: 1875-1883.
10. Davidson, W. S., and T. B. Thompson. 2007. The structure of apolipoprotein A-I in high density lipoproteins. J. Biol. Chem. 282: 22249-22253.
11. Guidotti,G. 1972. Membrane proteins. Annu. Rev. Biochem. 41: 731-752.
12. Eichacker, L. A., B. Granvogl, O. Mirus, B. C. Muller, C. Miess, and E. Schleiff. 2004. Hiding behind hydrophobicity. Transmembrane segments in mass spectrometry. J. Biol. Chem. 279: 50915-50922.
13. Speers, A. E., and C. C. Wu. 2007. Proteomics of integral membrane proteins-theory and application. Chem. Rev. 107: 3687-3714.
14. Lu, B., D. B. McClatchy, J. Y. Kim, and J. R. Yates III. 2008. Strategies for shotgun identification of integral membrane proteins by tandem mass spectrometry. Proteomics. 8: 3947-3955.
15. Zhang, L., J. Xie, X. Wang, X. Liu, X. Tang, R. Cao, W. Hu, S. Nie, C. Fan, and S. Liang. 2005. Proteomic analysis of mouse liver plasma membrane: use of differential extraction to enrich hydrophobic membrane proteins. Proteomics. 5: 4510-4524.
16. Zhang, L. J., X. E. Wang, X. Peng, Y. J. Wei, R. Cao, Z. Liu, J. X. Xiong, X. F. Yin, C. Ping, and S. Liang. 2006. Proteomic analysis of low-abundant integral plasma membrane proteins based on gels. Cell. Mol. Life Sci. 63: 1790-1804.
17. Chaney, L. K., and B. S. Jacobson. 1983. Coating cells with colloidal silica for high yield isolation of plasma membrane sheets and identification of transmembrane proteins. J. Biol. Chem. 258: 10062-10072.
18. Stolz, D. B., and B. S. Jacobson. 1992. Examination of transcellular membrane protein polarity of bovine aortic endothelial cells in vitro using the cationic colloidal silica microbead membrane-isolation procedure. J. Cell Sci. 103: 39-51.
19. Schindler, J., and H. G. Nothwang. 2006. Aqueous polymer two-phase systems: effective tools for plasma membrane proteomics. Proteomics. 6: 5409-5417.
20. Zhao, Y., W. Zhang, and Y. Kho. 2004. Proteomic analysis of integral plasma membrane proteins. Anal. Chem. 76: 1817-1823.
21. Sostaric, E., A. S. Georgiou, C. H. Wong, P. F. Watson, W. V. Holt, and A. Fazeli. 2006. Global profiling of surface plasma membrane proteome of oviductal epithelial cells. J. Proteome Res. 5: 3029-3037.
22. Nunomura, K., K. Nagano, C. Itagaki, M. Taoka, N. Okamura, Y. Yamauchi, S. Sugano, N. Takahashi, T. Izumi, and T. Isobe. 2005. Cell surface labeling and mass spectrometry reveal diversity of cell surface markers and signaling molecules expressed in undifferentiated mouse embryonic stem cells. Mol. Cell. Proteomics. 4: 1968-1976.
23. Ghosh, D., O. Krokhin, M. Antonovici, W. Ens, K. G. Standing, R. C. Beavis, and J. A.Wilkins. 2004. Lectin affinity as an approach to the proteomic analysis of membrane glycoproteins. J. Proteome Res. 3: 841-850.
24. Atwood III, J. A., T. Minning, F. Ludolf, A. Nuccio, D. B. Weatherly, G. Alvarez-Manilla, R. Tarleton, and R. Orlando. 2006. Glycoproteomics of Trypanosoma cruzi trypomastigotes using subcellular fractionation, lectin affinity, and stable isotope labeling. J. Proteome Res. 5: 3376-3384.
25. Zhang,H., X. J. Li, D. B.Martin, and R. Aebersold. 2003. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21: 660-666.
26. Josic, D., and J. G. Clifton. 2007. Mammalian plasma membrane proteomics. Proteomics. 7: 3010-3029.
27. Wessel, D., and U. I. Flugge. 1984. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 138: 141-143.
28. Stone, K. L., M. B. LoPresti, and K. R. Williams. 1990. Enzymatic digestion of proteins and HPLC peptide isolation at subnanomolar range. In Laboratory Methodology in Biochemistry: Amino Acid Analysis and Protein Sequencing. C. Fini, A. Floridi, and V. N. Finelli, editors. CRC Press, Boca Raton, FL. 181-206.
29. Bornsen, K. O., M. A. Gass, G. J. Bruin, J. H. von Adrichem, M. C. Biro, G. M. Kresbach, and M. Ehrat. 1997. Influence of solvents and detergents on matrix-assisted laser desorption/ionization mass spectrometry measurements of proteins and oligonucleotides. Rapid Commun. Mass Spectrom. 11: 603-609.
30. Rabilloud, T. 1998. Use of thiourea to increase the solubility of membrane proteins in two-dimensional electrophoresis. Electrophoresis. 19: 758-760.
31. Babu, G. J., D. Wheeler, O. Alzate, and M. Periasamy. 2004. Solubilization of membrane proteins for two-dimensional gel electrophoresis: identification of sarcoplasmic reticulum membrane proteins. Anal. Biochem. 325: 121-125.
32. Henningsen, R., B. L. Gale, K. M. Straub, and D. C. DeNagel. 2002. Application of zwitterionic detergents to the solubilization of integral membrane proteins for two-dimensional gel electrophoresis and mass spectrometry. Proteomics. 2: 1479-1488.
33. Molloy, M. P. 2000. Two-dimensional electrophoresis of membrane proteins using immobilized pH gradients. Anal. Biochem. 280: 1-10.
34. Molloy, M. P., B. R. Herbert, B. J. Walsh, M. I. Tyler, M. Traini, J. C. Sanchez, D. F. Hochstrasser, K. L. Williams, and A. A. Gooley. 1998. Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis. 19: 837-844.
35. Molloy, M. P., N. D. Phadke, J. R. Maddock, and P. C. Andrews. 2001. Two-dimensional electrophoresis and peptide mass fingerprinting of bacterial outer membrane proteins. Electrophoresis. 22: 1686-1696.
36. Rahbar, A. M., and C. Fenselau. 2005. Unbiased examination of changes in plasma membrane proteins in drug resistant cancer cells. J. Proteome Res. 4: 2148-2153.
37. Yu, Y. Q., M. Gilar, P. J. Lee, E. S. Bouvier, and J. C. Gebler. 2003. Enzyme-friendly, mass spectrometry-compatible surfactant for insolution enzymatic digestion of proteins. Anal. Chem. 75: 6023-6028.
38. Norris, J. L., M. J. Hangauer, N. A. Porter, and R. M. Caprioli. 2005. Nonacid cleavable detergents applied to MALDI mass spectrometry profiling of whole cells. J. Mass Spectrom. 40: 1319-1326.
39. Chen, E. I., D. McClatchy, S. K. Park, and J. R. Yates III. 2008. Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome. Anal. Chem. 80: 8694-8701.
40. Fischer, F., D. Wolters, M. Rogner, and A. Poetsch. 2006. Toward the complete membrane proteome: high coverage of integral membrane proteins through transmembrane peptide detection. Mol. Cell. Proteomics. 5: 444-453.
41. Russell, W. K., Z. Y. Park, and D. H. Russell. 2001. Proteolysis in mixed organic-aqueous solvent systems: applications for peptide mass mapping using mass spectrometry. Anal. Chem. 73: 2682-2685.
42. Strader, M. B., D. L. Tabb, W. J. Hervey, C. Pan, and G. B. Hurst. 2006. Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems. Anal. Chem. 78: 125-134.
43. Blonder, J., T. P. Conrads, L. R. Yu, A. Terunuma, G. M. Janini, H. J. Issaq, J. C. Vogel, and T. D. Veenstra. 2004. A detergent- and cyanogen bromide-free method for integral membrane proteomics: application to Halobacterium purple membranes and the human epidermal membrane proteome. Proteomics. 4: 31-45.
44. Blonder, J., M. B. Goshe, R. J. Moore, L. Pasa-Tolic, C. D. Masselon, M. S. Lipton, and R. D. Smith. 2002. Enrichment of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry. J. Proteome Res. 1: 351-360.
45. Washburn, M. P., D. Wolters, and J. R. Yates III. 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19: 242-247.
46. Speers, A. E., A. R. Blackler, and C. C. Wu. 2007. Shotgun analysis of integral membrane proteins facilitated by elevated temperature. Anal. Chem. 79: 4613-4620.
47. Prinz, T., J. Muller, K. Kuhn, J. Schafer, A. Thompson, J. Schwarz, and C. Hamon. 2004. Characterization of low abundant membrane proteins using the protein sequence tag technology. J. Proteome Res. 3: 1073-1081.
48. Zubarev, R. A., A. R. Zubarev, and M. M. Savitski. 2008. Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet? J. Am. Soc. Mass Spectrom. 19: 753-761.
49. Good, D. M., M. Wirtala, G. C. McAlister, and J. J. Coon. 2007. Performance characteristics of electron transfer dissociation mass spectrometry. Mol. Cell. Proteomics. 6: 1942-1951.
50. Han, C. L., C. W. Chien, W. C. Chen, Y. R. Chen, C. P. Wu, H. Li, and Y. J. Chen. 2008. A multiplexed quantitative strategy for membrane proteomics: opportunities for mining therapeutic targets for autosomal dominant polycystic kidney disease. Mol. Cell. Proteomics. 7: 1983-1997.
51. Howell, K. E., and G. E. Palade. 1982. Hepatic Golgi fractions resolved into membrane and content subfractions. J. Cell Biol. 92: 822-832.
52. Wu, C. C., and J. R. Yates III. 2003. The application of mass spectrometry to membrane proteomics. Nat. Biotechnol. 21: 262-267.
53. Laberge, M. A., K. J. Moore, and M. W. Freeman. 2005. Atherosclerosis and innate immune signaling. Ann. Med. 37: 130-140.
54. Barter, P. J., S. Nicholls, K. A. Rye, G. M. Anantharamaiah, M. Navab, and A. M. Fogelman. 2004. Antiinflammatory properties of HDL. Circ. Res. 95: 764-772.
55. Shiflett, A. M., J. R. Bishop, A. Pahwa, and S. L. Hajduk. 2005. Human high density lipoproteins are platforms for the assembly of multi-component innate immune complexes. J. Biol. Chem. 280: 32578-32585.
56. Vaisar, T., S. Pennathur, P. S. Green, S. A. Gharib, A. N. Hoofnagle, M. C. Cheung, J. Byun, S. Vuletic, S. Kassim, P. Singh, et al. 2007. Shotgun proteomics implicates protease inhibition and complement activation in the antiinflammatory properties of HDL. J. Clin. Invest. 117: 746-756.
57. Havel, R. J., H. A. Eder, and J. H. Bragdon. 1955. The distribution and chemical composition of ultracentrifugally separated lipoproteins in human serum. J. Clin. Invest. 34: 1345-1353.
58. Prassl, R., and P. Laggner. 2009. Molecular structure of low density lipoprotein: current status and future challenges. Eur. Biophys. J. 38: 145-158.
59. Karlsson, H., P. Leanderson, C. Tagesson, and M. Lindahl. 2005. Lipoproteomics I: mapping of proteins in low-density lipoprotein using two-dimensional gel electrophoresis and mass spectrometry. Proteomics. 5: 551-565.
60. Kunitake, S. T., C. T. Carilli, K. Lau, A. A. Protter, J. Naya-Vigne, and J. P. Kane. 1994. Identification of proteins associated with apolipoprotein A-I-containing lipoproteins purified by selected-affinity immunosorption. Biochemistry. 33: 1988-1993.
61. Zechner, R., R. Moser, and G. M. Kostner. 1986. Isolation of pure LpB from human serum. J. Lipid Res. 27: 681-686.
62. Kostner, G. M. 1983. Apolipoproteins and lipoproteins of human plasma: significance in health and in disease. Adv. Lipid Res. 20: 1-43.
63. Folch, J., M. Lees, and G. H. Sloane Stanley. 1957. A simple method for the isolation and purification of total lipides from animal tissues. J. Biol. Chem. 226: 497-509.
64. Rezaee, F., B. Casetta, J. H. Levels, D. Speijer, and J. C. Meijers. 2006. Proteomic analysis of high-density lipoprotein. Proteomics. 6: 721-730.
65. Farwig, Z. N., A. V. Campbell, and R. D. Macfarlane. 2003. Analysis of high-density lipoprotein apolipoproteins recovered from specific immobilized pH gradient gel pI domains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Chem. 75: 3823-3830.
66. Ogorzalek Loo, R. R., L. Yam, J. A. Loo, and V. N. Schumaker. 2004. Virtual two-dimensional gel electrophoresis of high-density lipoproteins. Electrophoresis. 25: 2384-2391.
67. Stahlman, M., P. Davidsson, I. Kanmert, B. Rosengren, J. Boren, B. Fagerberg, and G. Camejo. 2008. Proteomics and lipids of lipoproteins isolated at low salt concentrations in D2O/sucrose or in KBr. J. Lipid Res. 49: 481-490.
68. Davidsson, P., J. Hulthe, B. Fagerberg, B. M. Olsson, C. Hallberg, B. Dahllof, and G. Camejo. 2005. A proteomic study of the apolipoproteins in LDL subclasses in patients with the metabolic syndrome and type 2 diabetes. J. Lipid Res. 46: 1999-2006.
69. Levels, J. H., B. Bleijlevens, F. Rezaee, J. M. Aerts, and J. C. Meijers. 2007. SELDI-TOF mass spectrometry of high-density lipoprotein. Proteome Sci. 5: 15.
70. Mancone, C., L. Amicone, G. M. Fimia, E. Bravo, M. Piacentini, M. Tripodi, and T. Alonzi. 2007. Proteomic analysis of human very low-density lipoprotein by two-dimensional gel electrophoresis and MALDI-TOF/TOF. Proteomics. 7: 143-154.
71. Heller, M., E. Schlappritzi, D. Stalder, J. M. Nuoffer, and A. Haeberli. 2007. Compositional protein analysis of high density lipoproteins in hypercholesterolemia by shotgun LC-MS/MS and probabilistic peptide scoring. Mol. Cell. Proteomics. 6: 1059-1072.
72. Heller, M., D. Stalder, E. Schlappritzi, G. Hayn, U. Matter, and A. Haeberli. 2005. Mass spectrometry-based analytical tools for the molecular protein characterization of human plasma lipoproteins. Proteomics. 5: 2619-2630.
73. Green, P. S., T. Vaisar, S. Pennathur, J. J. Kulstad, A. B. Moore, S. Marcovina, J. Brunzell, R. H. Knopp, X-Q. Zhao, and J. W. Heinecke. 2008. Combined statin and niacin therapy remodels the high-density lipoprotein proteome. Circulation. 118: 1259-1267.