Nonionic detergent phase extraction for the proteomic analysis of heart membrane proteins using label-free LC-MS

Proteomics

Volumn 8, Issue 18, 2008, Pages 3895-3905

  Donoghue, Pamela M ^a   Hughes, Chris ^b   Vissers, Johannes P C ^b   Langridge, James I ^b   Dunn, Michael J ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b WATERS CORPORATION   (United States)

Author keywords

Heart; LC MS and GRAVY (hydrophobicity) annotation; Mass spectrometry; Membrane proteins; Protein identification

Indexed keywords

DETERGENT; MEMBRANE PROTEIN; PROTEOME; TRITON X 114;

ARTICLE; EXTRACTION; HEART MUSCLE FIBER MEMBRANE; HYDROPHOBICITY; LIQUID CHROMATOGRAPHY; NONHUMAN; NUCLEOTIDE SEQUENCE; PILOT STUDY; PRIORITY JOURNAL; PROTEOMICS; SCORING SYSTEM; SEPARATION TECHNIQUE;

CHROMATOGRAPHY, LIQUID; DETERGENTS; HEART VENTRICLES; HUMANS; MASS SPECTROMETRY; MEMBRANE PROTEINS; PROTEOMICS;

EID: 53549100778     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800116     Document Type: Article

References (39)

1. McGregor, E., Dunn, M. J., Proteomics of the heart: Unraveling disease. Circ. Res. 2006, 98, 309-321.
2. Rabilloud, T., Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains. Proteomics 2002, 2, 3-10.
3. Corthals, G. L., Wasinger, V. C., Hochstrasser, D. F., Sanchez, J. C., The dynamic range of protein expression: A challenge for proteomic research. Electrophoresis 2000, 21, 1104-1115.
4. Wu, C. C., Yates, J. R., III, The application of mass spectrometry to membrane proteomics. Nat. Biotechnol. 2003, 21, 262-267.
5. Wu, C. C., MacCoss, M. J., Howell, K. E., Yates, J. R., III, A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 2003, 21, 532-538.
6. Gorg, A., Weiss, W., Dunn, M. J., Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004, 4, 3665-3685.
7. Simpson, R. J., Connolly, L. M., Eddes, J. S., Pereira, J. J. et al., Proteomic analysis of the human colon carcinoma cell line (LIM 1215): Development of a membrane protein database. Electrophoresis 2000, 21, 1707-1732.
8. Blonder, J., Terunuma, A., Conrads, T. P., Chan, K. C. et al., A proteomic characterization of the plasma membrane of human epidermis by high-throughput mass spectrometry. J. Invest. Dermatol. 2004, 123, 691-699.
9. Cutillas, P. R., Biber, J., Marks, J., Jacob, R. et al., Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex. Proteomics 2005, 5, 101-112.
10. Zhao, Y., Zhang, W., White, M. A., Zhao, Y., Capillary high-performance liquid chromatography/mass spectrometric analysis of proteins from affinity-purified plasma membrane. Anal. Chem. 2003, 75, 3751-3757.
11. Clifton, J. G., Li, X., Reutter, W., Hixson, D. C., Josic, D., Comparative proteomics of rat liver and Morris hepatoma 7777 plasma membranes. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 849, 293-301.
12. Josic, D., Clifton, J. G., Mammalian plasma membrane proteomics. Proteomics 2007, 7, 3010-3029.
13. Bordier, C., Phase separation of integral membrane proteins in Triton X-114 solution. J. Biol. Chem. 1981, 256, 1604-1607.
14. Bordier, C., Loomis, W. F., The major developmentally regulated protein complex in membranes of Dictyostelium. J. Biol. Chem. 1978, 253, 5133-5139.
15. Bordier, C., Garavito, R. M., Armbruster, B., Biochemical and structural analyses of microtubules in the pellicular membrane of Leishmania tropica. J. Protozool. 1982, 29, 560-565.
16. Etges, R., Bouvier, J., Bordier, C., The major surface protein of Leishmania promastigotes is anchored in the membrane by a myristic acid-labeled phospholipid. EMBO J. 1986, 5, 597-601.
17. Boylan, G. M., Pryde, J. G., Dobbs, L. G., McElroy, M. C., Identification of a novel antigen on the apical surface of rat alveolar epithelial type II and Clara cells. Am. J. Physiol. Lung Cell. Mol. Physiol. 2001, 280, L1318-1326.
18. Fournier, D., Berge, J. B., Cardoso de Almeida, M. L., Bordier, C., Acetylcholinesterases from Musca domestica and Drosophila melanogaster brain are linked to membranes by a glycophospholipid anchor sensitive to an endogenous phospholipase. J. Neurochem. 1988, 50, 1158-1163.
19. Percy, J. M., Pryde, J. G., Apps, D. K., Isolation of ATPase I, the proton pump of chromaffin-granule membranes. Biochem. J. 1985, 231, 557-564.
20. Pryde, J. G., A group of integral membrane proteins of the rat liver Golgi contains a conserved protein of 100 kDa. J. Cell Sci. 1994, 107, 3425-3436.
21. Villeneuve, C., Etienne, G., Abadie, V., Montrozier, H. et al., Surface-exposed glycopeptidolipids of Mycobacterium smegmatis specifically inhibit the phagocytosis of mycobacteria by human macrophages. Identification of a novel family of glycopeptidolipids. J. Biol. Chem. 2003, 278, 51291-51300.
22. Mattow, J., Siejak, F., Hagens, K., Schmidt, F. et al., An improved strategy for selective and efficient enrichment of integral plasma membrane proteins of mycobacteria. Proteomics 2007, 7, 1687-1701.
23. Yu, Y Q., Gilar, M., Lee, P. J., Bouvier, E. S., Gebier, J. C., Enzyme-friendly, mass spectrometry-compatible surfactant for in-solution enzymatic digestion of proteins. Anal. Chem. 2003, 75, 6023-6028.
24. Bradford, M. M., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976, 72, 248-254.
25. Silva, J. C., Denny, R., Dorschel, C. A., Gorenstein, M. et al., Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 2005, 77, 2187-2200.
26. Skilling, J., Denny, R., Richardson, K., Young, P. et al., Prob-seq- A fragmentation model for interpretation of electro-spray tandem mass spectrometry data. Comp. Funct. Genom. 2004, 5, 61-68.
27. Vissers, J. P., Langridge, J. I., Aerts, J. M., Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol. Cell. Proteomics 2007, 6, 755-766.
28. Kyte, J., Doolittle, R. F., A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982, 157, 105-132.
29. Wilkins, M. R., Lindskog, L., Gasteiger, E., Bairoch, A. et al., Detailed peptide characterization using PEPTIDEMASS-a World-Wide-Web-accessible tool. Electrophoresis 1997, 18, 403-408.
30. Kall, L., Krogh, A., Sonnhammer, E. L., A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 2004, 338, 1027-1036.
31. Towbin, H., Staehelin, T., Gordon, J., Electrophoretic transfer of proteins from Polyacrylamide gels to nitrocellulose sheets: Procedure and some applications. Proc. Natl. Acad. Sci. USA 1979, 76, 4350-4354.
32. E: A virtue of parallel MS acquisition. Mol. Cell. Proteomics 2006, 5, 144-156.
33. Horgan, G. W., Sample size and replication in 2D gel electrophoresis studies. J. Proteome Res. 2007, 6, 2884-2887.
34. Karp, N. A., Spencer, M., Lindsay, H., O'Dell, K., Lilley, K. S., Impact of replicate types on proteomic expression analysis. J. Proteome Res. 2005, 4, 1867-1871.
35. Molloy, M. P., Donohoe, S., Brzezinski, E. E., Kilby, G. W. et al., Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable coded affinity tag mass spectrometry for proteomic profiling. Proteomics 2005, 5, 1204-1208.
36. Hunt, S. M., Thomas, M. R., Sebastian, L. T., Pedersen, S. K. et al., Optimal replication and the importance of experimental design for gel-based quantitative proteomics. J. Proteome Res. 2005, 4, 809-819.
37. Santoni, V., Molloy, M., Rabilloud, T., Membrane proteins and proteomics: Un amour impossible? Electrophoresis 2000, 27, 1054-1070.
38. Rabilloud, T., Membrane proteins ride shotgun. Nat. Biotechnol. 2003, 21, 508-510.
39. Hopkins, A. M., Baird, A. W., Nusrat, A., ICAM-1: Targeted docking for exogenous as well as endogenous ligands. Adv. Drug Deliv. Rev. 2004, 56, 763-778.