A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells

Proteomics

Volumn 8, Issue 19, 2008, Pages 4036-4053

  Dormeyer, Wilma ^a,c   Van Hoof, Dennis ^b   Mummery, Christine L ^b   Krijgsveld, Jeroen ^a   Heck, Albert J R ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b HUBRECHT INSTITUTE   (Netherlands)

^c ROCHE DIAGNOSTICS GMBH   (Germany)

Author keywords

Membrane proteins; Plasma membrane proteins; Stem cells

Indexed keywords

MEMBRANE PROTEIN; PLASMA PROTEIN; STAGE SPECIFIC EMBRYO ANTIGEN 3; STAGE SPECIFIC EMBRYO ANTIGEN 4;

CELL DIFFERENTIATION; CELL MEMBRANE; CELL PROLIFERATION; CHROMOSOME ABERRATION; DEGLYCOSYLATION; EMBRYO DEVELOPMENT; EMBRYONAL CARCINOMA; EMBRYONIC STEM CELL; FUNCTIONAL PROTEOMICS; HUMAN; NONHUMAN; PRACTICE GUIDELINE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; REVIEW;

CELL MEMBRANE; EMBRYONAL CARCINOMA STEM CELLS; EMBRYONIC STEM CELLS; HUMANS; MEMBRANE PROTEINS; PROTEIN DENATURATION; PROTEOMICS; TRYPSIN;

EID: 55749106911     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800143     Document Type: Review

References (128)

1. Alberts, B., Johnson, A., Lewis, J., Raff, M. et al., (Eds.), Molecular Biology of the Cell, Garland Science, New York 2002.
2. Petty, H. R., Molecular Biology of Membranes: Structure and Function, Springer Verlag, Plenum Press, New York 2007.
3. Laude, A. J., Prior, I. A., Plasma membrane microdomains: Organization, function and trafficking. Mol. Membr. Biol. 2004, 21, 193-205.
4. Banfi, C., Brioschi, M., Wait, R., Begum, S. et al., Proteomic analysis of membrane microdomains derived from both failing and nonfailing human hearts. Proteomics 2006, 6, 1976-1988.
5. Cheng, Z. J., Singh, R. D., Marks, D. L., Pagano, R. E., Membrane-microdomains, caveolae, and caveolar endocytosis of sphingolipids. Mol. Membr. Biol. 2006, 23, 101-110.
6. Raimondo, F., Ceppi, P., Guidi, K., Masserini, M. et al., Proteomics of plasma membrane microdomains. Expert. Rev. Proteomics 2005, 2, 793-807.
7. Hopkins, A. L., Groom, C. R., Target analysis: A priori assessment of druggability. Ernst Schering Research Foundation Workshop 2003, pp. 11-17.
8. Rabilloud, T., Membrane proteins ride shotgun. Nat. Biotechnol. 2003, 21, 508-510.
9. Russ, A. P., Lampel, S., The druggable genome: An update. Drug Discov. Today 2005, 10, 1607-1610.
10. Raman, P., Cherezov, V., Caffrey, M., The Membrane Protein Data Bank. Cell Mol. Life Sci. 2006, 63, 36-51.
11. Nyholm, T. K., Ozdirekcan, S., Killian, J. A., How protein transmembrane segments sense the lipid environment. Biochemistry 2007, 46, 1457-1465.
12. Speers, A. E., Wu, C. C., Proteomics of integral membrane proteins - theory and application. Chem. Rev. 2007, 107, 3687-3714.
13. Mackenzie, K. R., Folding and stability of alpha-helical integral membrane proteins. Chem. Rev. 2006, 106, 1931-1977.
14. Engelman, D. M., Chen, Y., Chin, C. N., Curran, A. R. et al., Membrane protein folding: Beyond the two stage model. FEBS Lett. 2003, 555, 122-125.
15. Rossant, J., Stem cells and lineage development in the mammalian blastocyst. Reproduction, fertility, and development 2007, 19, 111-118.
16. Damjanov, I., The road from teratocarcinoma to human embryonic stem cells. Stem Cell Rev. 2005, 1, 273-276.
17. Andrews, P. W., Matin, M. M., Bahrami, A. R., Damjanov, I. et al., Embryonic stem (ES) cells and embryonal carcinoma (EC) cells: Opposite sides of the same coin. Biochem. Soc. Trans. 2005, 33, 1526-1530.
18. Evans, M. J., Kaufman, M. H., Establishment in culture of pluripotential cells from mouse embryos. Nature 1981, 292, 154-156.
19. Martin, G. R., Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl. Acad. Sci. USA 1981, 78, 7634-7638.
20. Thomson, J. A., Itskovitz-Eldor, J., Shapiro, S. S., Waknitz, M. A. et al., Embryonic stem cell lines derived from human blastocysts. Science 1998, 282, 1145-1147.
21. Adewumi, O., Aflatoonian, B., Ahrlund-Richter, L., Amit, M. et al., Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nat. Biotechnol. 2007, 25, 803-816.
22. Andrews, P. W., Benvenisty, N., McKay, R., Pera, M. F. et al., The International Stem Cell Initiative: Toward benchmarks for human embryonic stem cell research. Nat. Biotechnol. 2005, 23, 795-797.
23. Bradley, A., Evans, M., Kaufman, M. H., Robertson, E., Formation of germ-line chimaeras from embryo-derived teratocarcinoma cell lines. Nature 1984, 309, 255-256.
24. Reubinoff, B. E., Pera, M. F., Fong, C. Y., Trounson, A., Bongso, A., Embryonic stem cell lines from human blastocysts: Somatic differentiation in vitro. Nat. Biotechnol. 2000, 18, 399-404.
25. Cowan, C. A., Klimanskaya, I., McMahon, J., Atienza, J. et al., Derivation of embryonic stem-cell lines from human blastocysts. N. Engl. J. Med. 2004, 350, 1353-1356.
26. Ginis, I., Luo, Y., Miura, T., Thies, S. et al., Differences between human and mouse embryonic stem cells. Dev. Biol. 2004, 269, 360-380.
27. Brons, I. G., Smithers, L. E., Trotter, M. W., Rugg-Gunn, P. et al., Derivation of pluripotent epiblast stem cells from mammalian embryos. Nature 2007, 448, 191-195.
28. Tesar, P. J., Chenoweth, J. G., Brook, F. A., Davies, T. J. et al., New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature 2007, 448, 196-199.
29. Shevinsky, L. H., Knowles, B. B., Damjanov, I., Solter, D., Monoclonal antibody to murine embryos defines a stage-specific embryonic antigen expressed on mouse embryos and human teratocarcinoma cells. Cell 1982, 30, 697-705.
30. Kannagi, R., Levery, S. B., Ishigami, F., Hakomori, S. et al., New globoseries glycosphingolipids in human teratocarcinoma reactive with the monoclonal antibody directed to a developmentally regulated antigen, stage-specific embryonic antigen 3. J. Biol. Chem. 1983, 258, 8934-8942.
31. Andrews, P. W., Banting, G., Damjanov, I., Arnaud, D., Avner, P., Three monoclonal antibodies defining distinct differentiation antigens associated with different high molecular weight polypeptides on the surface of human embryonal carcinoma cells. Hybridoma 1984, 3, 347-361.
32. Samaniego, F., Rodriguez, E., Houldsworth, J., Murty, V. V. et al., Cytogenetic and molecular analysis of human male germ cell tumors: Chromosome 12 abnormalities and gene amplification. Genes Chromosomes Cancer 1990, 1, 289-300.
33. Reuter, V. E., Origins and molecular biology of testicular germ cell tumors. Mod. Pathol. 2005, 18, S51-S60.
34. Baker, D. E., Harrison, N. J., Maltby, E., Smith, K. et al., Adaptation to culture of human embryonic stem cells and oncogenesis in vivo. Nat. Biotechnol. 2007, 25, 207-215.
35. Baharvand, H., Hajheidari, M., Ashtiani, S. K., Salekdeh, G. H., Proteomic signature of human embryonic stem cells. Proteomics 2006, 6, 3544-3549.
36. Van Hoof, D., Mummery, C. L., Heck, A. J., Krijgsveld, J., Embryonic stem cell proteomics. Expert Rev. Proteomics 2006, 3, 427-437.
37. Wu, C. C., Yates, J. R., III, The application of mass spectrometry to membrane proteomics. Nat. Biotechnol. 2003, 21, 262-267.
38. Josic, D., Clifton, J. G., Mammalian plasma membrane proteomics. Proteomics 2007, 7, 3010-3029.
39. Zhao, Y., Zhang, W., Kho, Y., Zhao, Y., Proteomic analysis of integral plasma membrane proteins. Anal. Chem. 2004, 76, 1817-1823.
40. Santoni, V., Molloy, M., Rabilloud, T., Membrane proteins and proteomics: Un amour impossible? Electrophoresis 2000, 21, 1054-1070.
41. Macher, B. A., Yen, T. Y., Proteins at membrane surfaces-a review of approaches. Mol. BioSyst. 2007, 3, 705-713.
42. Whitelegge, J., Halgand, F., Souda, P., Zabrouskov, V., Topdown mass spectrometry of integral membrane proteins. Expert Rev. Proteomics 2006, 3, 585-596.
43. Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
44. Mann, M., Hendrickson, R. C., Pandey, A., Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 2001, 70, 437-473.
45. McDonald, W. H., Yates, J. R., III, Shotgun proteomics: Integrating technologies to answer biological questions. Curr. Opin. Mol. Ther. 2003, 5, 302-309.
46. Zhang, L., Xie, J., Wang, X., Liu, X. et al., Proteomic analysis of mouse liver plasma membrane: Use of differential extraction to enrich hydrophobic membrane proteins. Proteomics 2005, 5, 4510-4524.
47. Josic, D., Brown, M. K., Huang, F., Callanan, H. et al., Use of selective extraction and fast chromatographic separation combined with electrophoretic methods for mapping of membrane proteins. Electrophoresis 2005, 26, 2809-2822.
48. Clifton, J. G., Li, X., Reutter, W., Hixson, D. C., Josic, D., Comparative proteomics of rat liver and Morris hepatoma 7777 plasmamembranes. J. Chromatogr. B: Analyt. Technol. Biomed. Life Sci. 2007, 849, 293-301.
49. Ahram, M., Litou, Z. I., Fang, R., Al-Tawallbeh, G., Estimation of membrane proteins in the human proteome. In Silico Biol. 2006, 6, 379-386.
50. Wallin, E., von Heijne, G., Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 1998, 7, 1029-1038.
51. Le Naour, F., Andre, M., Boucheix, C., Rubinstein, E., Membrane microdomains and proteomics: Lessons from tetraspanin microdomains and comparison with lipid rafts. Proteomics 2006, 6, 6447-6454.
52. Grant, K. J., Wu, C. C., Advances in neuromembrane proteomics: Efforts towards a comprehensive analysis of membrane proteins in the brain. Brief. Funct. Genomics Proteomics 2007, 6, 59-69.
53. Stockwin, L. H., Blonder, J., Bumke, M. A., Lucas, D. A. et al., Proteomic analysis of plasma membrane from hypoxia-adapted malignant melanoma. J. Proteome Res. 2006, 5, 2996-3007.
54. 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.
55. Zhang, W., Zhou, G., Zhao, Y., White, M. A., Zhao, Y., Affinity enrichment of plasma membrane for proteomics analysis. Electrophoresis 2003, 24, 2855-2863.
56. 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.
57. Durr, E., Yu, J., Krasinska, K. M., Carver, L. A. et al., Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat. Biotechnol. 2004, 22, 985-992.
58. Elortza, F., Mohammed, S., Bunkenborg, J., Foster, L. J. et al., Modification-specific proteomics of plasma membrane proteins: Identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment. J. Proteome Res. 2006, 5, 935-943.
59. Nunomura, K., Nagano, K., Itagaki, C., Taoka, M. et al., 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 2005, 4, 1968-1976.
60. Rahbar, A. M., Fenselau, C., Integration of Jacobson's pellicle method into proteomic strategies for plasma membrane proteins. J. Proteome Res. 2004, 3, 1267-1277.
61. Schindler, J., Lewandrowski, U., Sickmann, A., Friauf, E., Nothwang, H. G., Proteomic analysis of brain plasma membranes isolated by affinity two-phase partitioning. Mol. Cell. Proteomics 2006, 5, 390-400.
62. Cao, R., Li, X., Liu, Z., Peng, X. et al., Integration of a two-phase partition method into proteomics research on rat liver plasma membrane proteins. J. Proteome Res. 2006, 5, 634-642.
63. Morre, D. M., Morre, D. J., Aqueous two-phase partition applied to the isolation of plasma membranes and Golgi apparatus from cultured mammalian cells. J. Chromatogr. B: Biomed. Sci. Appl. 2000, 743, 377-387.
64. Chen, P., Li, X., Sun, Y., Liu, Z. et al., Proteomic analysis of rat hippocampal plasma membrane: Characterization of potential neuronal-specific plasma membrane proteins. J. Neurochem. 2006, 98, 1126-1140.
65. 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.
66. Lawson, E. L., Clifton, J. G., Huang, F., Li, X. et al., Use of magnetic beads with immobilized monoclonal antibodies for isolation of highly pure plasma membranes. Electrophoresis 2006, 27, 2747-2758.
67. Stasyk, T., Huber, L. A., Zooming in: Fractionation strategies in proteomics. Proteomics 2004, 4, 3704-3716.
68. Yates, J. R., III, Gilchrist, A., Howell, K. E., Bergeron, J. J., Proteomics of organelles and large cellular structures. Nat. Rev. Mol. Cell Biol. 2005, 6, 702-714.
69. Huber, L. A., Pfaller, K., Vietor, I., Organelle proteomics: Implications for subcellular fractionation in proteomics. Circ. Res. 2003, 92, 962-968.
70. Au, C. E., Bell, A. W., Gilchrist, A., Hiding, J. et al., Organellar proteomics to create the cell map. Curr. Opin. Cell Biol. 2007, 19, 376-385.
71. Andersen, J. S., Mann, M., Organellar proteomics: Turning inventories into insights. EMBO Rep. 2006, 7, 874-879.
72. Zahedi, R. P., Meisinger, C., Sickmann, A., Two-dimensional benzyldimethyl-n-hexadecylammonium chloride/SDS-PAGE for membrane proteomics. Proteomics 2005, 5, 3581-3588.
73. Zhou, M., Veenstra, T. D., Proteomic analysis of protein complexes. Proteomics 2007, 7, 2688-2697.
74. Chmelik, J., Applications of field-flow fractionation in proteomics: Presence and future. Proteomics 2007, 7, 2719-2728.
75. Nice, E. C., Rothacker, J., Weinstock, J., Lim, L., Catimel, B., Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis. J. Chromatogr. A 2007, 1168, 190-210; discussion 189.
76. Canas, B., Pineiro, C., Calvo, E., Lopez-Ferrer, D., Gallardo, J. M., Trends in sample preparation for classical and second generation proteomics. J. Chromatogr. A 2007, 1153, 235-258.
77. Wu, L., Han, D. K., Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev. Proteomics 2006, 3, 611-619.
78. Bhuyan, A. K., Protein stabilization by urea and guanidine hydrochloride. Biochemistry 2002, 41, 13386-13394.
79. Moglich, A., Krieger, F., Kiefhaber, T., Molecular basis for the effect of urea and guanidinium chloride on the dynamics of unfolded polypeptide chains. J. Mol. Biol. 2005, 345, 153-162.
80. Castellanos-Serra, L., Paz-Lago, D., Inhibition of unwanted proteolysis during sample preparation: Evaluation of its efficiency in challenge experiments. Electrophoresis 2002, 23, 1745-1753.
81. Gorg, A., Weiss, W., Dunn, M. J., Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004, 4, 3665-3685.
82. Righetti, P. G., Real and imaginary artefacts in proteome analysis via two-dimensional maps. J. Chromatogr. B: Analyt. Technol. Biomed. Life Sci. 2006, 841, 14-22.
83. Rappsilber, J., Ishihama, Y., Mann, M., Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 2003, 75, 663-670.
84. Washburn, M. P., Wolters, D., Yates, J. R., III, Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242-247.
85. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., Gygi, S. P., Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J. Proteome Res. 2003, 2, 43-50.
86. Nielsen, P. A., Olsen, J. V., Podtelejnikov, A. V., Andersen, J. R. et al., Proteomic mapping of brain plasma membrane proteins. Mol. Cell. Proteomics 2005, 4, 402-408.
87. Pasini, E. M., Kirkegaard, M., Mortensen, P., Lutz, H. U. et al., In-depth analysis of the membrane and cytosolic proteome of red blood cells. Blood 2006, 108, 791-801.
88. Molina, H., Horn, D. M., Tang, N., Mathivanan, S., Pandey, A., Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 2007, 104, 2199-2204.
89. Guerrero, C., Tagwerker, C., Kaiser, P., Huang, L., An integrated mass spectrometry-based proteomic approach: Quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol. Cell. Proteomics 2006, 5, 366-378.
90. Garavito, R. M., Ferguson-Miller, S., Detergents as tools in membrane biochemistry. J. Biol. Chem. 2001, 276, 32403-32406.
91. Everberg, H., Leiding, T., Schioth, A., Tjerneld, F., Gustavsson, N., Efficient and nondenaturing membrane solubilization combined with enrichment of membrane protein complexes by detergent/polymer aqueous two-phase partitioning for proteome analysis. J. Chromatogr. A 2006, 1122, 35-46.
92. Everberg, H., Sivars, U., Emanuelsson, C., Persson, C. et al., Protein prefractionation in detergent-polymer aqueous two-phase systems for facilitated proteomic studies of membrane proteins. J. Chromatogr. A 2004, 1029, 113-124.
93. McCarthy, F. M., Burgess, S. C., van den Berg, B. H., Koter, M. D., Pharr, G. T., Differential detergent fractionation for non-electrophoretic eukaryote cell proteomics. J. Proteome Res. 2005, 4, 316-324.
94. Chevallet, M., Santoni, V., Poinas, A., Rouquie, D. et al., New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis 1998, 19, 1901-1909.
95. Rabilloud, T., Blisnick, T., Heller, M., Luche, S. et al., Analysis of membrane proteins by two-dimensional electrophoresis: Comparison of the proteins extracted from normal or Plasmodium falciparum-infected erythrocyte ghosts. Electrophoresis 1999, 20, 3603-3610.
96. Reynolds, J. A., Tanford, C., The gross conformation of protein-sodium dodecyl sulfate complexes. J. Biol. Chem. 1970, 245, 5161-5165.
97. Reynolds, J. A., Tanford, C., Binding of dodecyl sulfate to proteins at high binding ratios. Possible implications for the state of proteins in biological membranes. Proc. Natl. Acad. Sci. USA 1970, 66, 1002-1007.
98. Bosserhoff, A., Wallach, J., Frank, R. W., Micropreparative separation of peptides derived from sodium dodecyl sulphate-solubilized proteins. J. Chromatogr. 1989, 473, 71-77.
99. Zischka, H., Gloeckner, C. J., Klein, C., Willmann, S. et al., Improved mass spectrometric identification of gel-separated hydrophobic membrane proteins after sodium dodecyl sulfate removal by ion-pair extraction. Proteomics 2004, 4, 3776-3782.
100. Loo, R. R., Dales, N., Andrews, P. C., Surfactant effects on protein structure examined by electrospray ionization mass spectrometry. Protein Sci. 1994, 3, 1975-1983.
101. Braun, R. J., Kinkl, N., Beer, M., Ueffing, M., Two-dimensional electrophoresis of membrane proteins. Anal. Bioanal. Chem. 2007, 389, 1033-1045.
102. Lu, X., Zhu, H., Tube-gel digestion: A novel proteomic approach for high throughput analysis of membrane proteins. Mol. Cell. Proteomics 2005, 4, 1948-1958.
103. Scharnagl, C., Reif, M., Friedrich, J., Stability of proteins: Temperature, pressure and the role of the solvent. Biochim. Biophys. Acta 2005, 1749, 187-213.
104. Pace, C. N., Trevino, S., Prabhakaran, E., Scholtz, J. M., Protein structure, stability and solubility in water and other solvents. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2004, 359, 1225-1234; discussion 1234-1225.
105. Simon, L. M., Kotorman, M., Garab, G., Laczko, I., Structure and activity of alpha-chymotrypsin and trypsin in aqueous organic media. Biochem. Biophys. Res. Commun. 2001, 280, 1367-1371.
106. Russell, W. K., Park, Z. Y., Russell, D. H., Proteolysis in mixed organic-aqueous solvent systems: Applications for peptide mass mapping using mass spectrometry. Anal. Chem. 2001, 73, 2682-2685.
107. Blonder, J., Conrads, T. P., Yu, L. R., Terunuma, A. et al., A detergent- and cyanogen bromide-free method for integral membrane proteomics: Application to Halobacterium purple membranes and the human epidermal membrane proteome. Proteomics 2004, 4, 31-45.
108. Fischer, F., Wolters, D., Rogner, M., Poetsch, A., Toward the complete membrane proteome: High coverage of integral membrane proteins through transmembrane peptide detection. Mol. Cell. Proteomics 2006, 5, 444-453.
109. Strader, M. B., Tabb, D. L., Hervey, W. J., Pan, C., Hurst, G. B., Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems. Anal. Chem. 2006, 78, 125-134.
110. Thiede, B., Hohenwarter, W., Krah, A., Mattow, J. et al., Peptide mass fingerprinting. Methods 2005, 35, 237-247.
111. Kapp, E. A., Schutz, F., Reid, G. E., Eddes, J. S. et al., Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 2003, 75, 6251-6264.
112. Paizs, B., Suhai, S., Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 2005, 24, 508-548.
113. Shi, Y., Xiang, R., Horvath, C., Wilkins, J. A., Quantitative analysis of membrane proteins from breast cancer cell lines BT474 and MCF7 using multistep solid phase mass tagging and 2D LC/MS. J. Proteome Res. 2005, 4, 1427-1433.
114. Xiang, R., Shi, Y., Dillon, D. A., Negin, B. et al., 2D LC/MS analysis of membrane proteins from breast cancer cell lines MCF7 and BT474. J. Proteome Res. 2004, 3, 1278-1283.
115. Harvey, D. J., Proteomic analysis of glycosylation: Structural determination of N- and O-linked glycans by mass spectrometry. Expert. Rev. Proteomics 2005, 2, 87-101.
116. Peter-Katalinic, J., Methods in enzymology: O-glycosylation of proteins. Methods Enzymol. 2005, 405, 139-171.
117. Edge, A. S., Deglycosylation of glycoproteins with trifluoromethanesulphonic acid: Elucidation of molecular structure and function. Biochem. J. 2003, 376, 339-350.
118. Wessel, D., Flugge, U. I., A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 1984, 138, 141-143.
119. Mastro, R., Hall, M., Protein delipidation and precipitation by tri-n-butylphosphate, acetone, and methanol treatment for isoelectric focusing and two-dimensional gel electrophoresis. Anal. Biochem. 1999, 273, 313-315.
120. le Maire, M., Deschamps, S., Moller, J. V., Le Caer, J. P., Rossier, J., Electrospray ionization mass spectrometry on hydrophobic peptides electroeluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis application to the topology of the sarcoplasmic reticulum Ca2+ ATPase. Anal. Biochem. 1993, 214, 50-57.
121. Borner, G. H., Sherrier, D. J., Weimar, T., Michaelson, L. V. et al., Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts. Plant Physiol. 2005, 137, 104-116.
122. Carboni, L., Piubelli, C., Righetti, P. G., Jansson, B., Domenici, E., Proteomic analysis of rat brain tissue: Comparison of protocols for two-dimensional gel electrophoresis analysis based on different solubilizing agents. Electrophoresis 2002, 23, 4132-4141.
123. Speers, A. E., Blackler, A. R., Wu, C. C., Shotgun analysis of integral membrane proteins facilitated by elevated temperature. Anal. Chem. 2007, 79, 4613-4620.
124. Kuhn, K., Thompson, A., Prinz, T., Muller, J. et al., Isolation of N-terminal protein sequence tags from cyanogen bromide cleaved proteins as a novel approach to investigate hydrophobic proteins. J. Proteome Res. 2003, 2, 598-609.
125. Liu, H., Lin, D., Yates, J. R., III, Multidimensional separations for protein/peptide analysis in the post-genomic era. BioTechniques 2002, 32, 898, 900, 902 passim.
126. Wu, C. C., MacCoss, M. J., Shotgun proteomics: Tools for the analysis of complex biological systems. Curr. Opin. Mol. Ther. 2002, 4, 242-250.
127. Yates, J. R., Cociorva, D., Liao, L., Zabrouskov, V., Performance of a linear ion trap-Orbitrap hybrid for peptide analysis. Anal. Chem. 2006, 78, 493-500.
128. van Laake, L. W., Hassink, R., Doevendans, P. A., Mummery, C., Heart repair and stem cells. J. Physiol. 2006, 577, 467-478.