Proteomics and the dynamic plasma membrane: Quo Vadis?

Proteomics

Volumn 10, Issue 22, 2010, Pages 3997-4011

  Sprenger, Richard R ^a   Jensen, Ole N ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Cell biology; MS; Plasma membrane proteomics; PTMs; Quantitative analysis; Transmembrane receptor

Indexed keywords

PROTEOME;

ARTICLE; CELL MEMBRANE; FUNCTIONAL PROTEOMICS; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN INTERACTION; QUANTITATIVE ANALYSIS;

ANIMALS; CELL MEMBRANE; HUMANS; MASS SPECTROMETRY; MEMBRANE PROTEINS; PROTEOMICS;

EUKARYOTA; MAMMALIA;

EID: 78449287281     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000312     Document Type: Article

References (131)

1. Singer, S. J., Nicolson, G. L., The fluid mosaic model of the structure of cell membranes. Science 1972, 175, 720-731.
2. Engelman, D. M., Membranes are more mosaic than fluid. Nature 2005, 438, 578-580.
3. Marguet, D., Lenne, P. F., Rigneault, H., He, H. T., Dynamics in the plasma membrane: how to combine fluidity and order. EMBO J. 2006, 25, 3446-3457.
4. Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
5. Domon, B., Aebersold, R., Mass spectrometry and protein analysis. Science 2006, 312, 212-217.
6. Andersen, J. S., Mann, M., Organellar proteomics: turning inventories into insights. EMBO Rep. 2006, 7, 874-879.
7. Jensen, O. N., Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell. Biol. 2006, 7, 391-403.
8. Premsler, T., Zahedi, R. P., Lewandrowski, U., Sickmann, A., Recent advances in yeast organelle and membrane proteomics. Proteomics 2009, 9, 4731-4743.
9. Komatsu, S., Plasma membrane proteome in Arabidopsis and rice. Proteomics 2008, 8, 4137-4145.
10. Josic, D., Clifton, J. G., Mammalian plasma membrane proteomics. Proteomics 2007, 7, 3010-3029.
11. Macher, B. A., Yen, T. Y., Proteins at membrane surfaces - a review of approaches. Mol. Biosyst. 2007, 3, 705-713.
12. Santoni, V., Molloy, M., Rabilloud, T., Membrane proteins and proteomics: un amour impossible? Electrophoresis 2000, 21, 1054-1070.
13. Anderson, R. G., Jacobson, K., A role for lipid shells in targeting proteins to caveolae, rafts, and other lipid domains. Science 2002, 296, 1821-1825.
14. Cordwell, S. J., Thingholm, T. E., Technologies for plasma membrane proteomics. Proteomics 2010, 10, 611-627.
15. Zheng, Y. Z., Foster, L. J., Biochemical and proteomic approaches for the study of membrane microdomains. J. Proteomics 2009, 72, 12-22.
16. Wu, C. C., MacCoss, M. J., Howell, K. E., Yates, J. R., 3rd, A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 2003, 21, 532-538.
17. Wu, C. C., Yates, J. R., 3rd, The application of mass spectrometry to membrane proteomics. Nat. Biotechnol. 2003, 21, 262-267.
18. Speers, A. E., Wu, C. C., Proteomics of integral membrane proteins - theory and application. Chem. Rev. 2007, 107, 3687-3714.
19. Helbig, A. O., Heck, A. J., Slijper, M., Exploring the membrane proteome - challenges and analytical strategies. J. Proteomics 2010, 73, 868-878.
20. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., Kuster, B., Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 2007, 389, 1017-1031.
21. Elliott, M. H., Smith, D. S., Parker, C. E., Borchers, C., Current trends in quantitative proteomics. J. Mass Spectrom. 2009, 44, 1637-1660.
22. Mueller, L. N., Brusniak, M. Y., Mani, D. R., Aebersold, R., An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 2008, 7, 51-61.
23. Panchaud, A., Affolter, M., Moreillon, P., Kussmann, M., Experimental and computational approaches to quantitative proteomics: status quo and outlook. J. Proteomics 2008, 71, 19-33.
24. Han, X., Aslanian, A., Yates, J. R. 3rd, Mass spectrometry for proteomics. Curr. Opin. Chem. Biol. 2008, 12, 483-490.
25. Yates, J. R., Ruse, C. I., Nakorchevsky, A., Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 2009, 11, 49-79.
26. Brunet, S., Thibault, P., Gagnon, E., Kearney, P. et al., Organelle proteomics: looking at less to see more. Trends Cell. Biol. 2003, 13, 629-638.
27. Sadowski, P. G., Groen, A. J., Dupree, P., Lilley, K. S., Sub-cellular localization of membrane proteins. Proteomics 2008, 8, 3991-4011.
28. Wiederhold, E., Veenhoff, L. M., Poolman, B., Slotboom, D. J., Proteomics of Saccharomyces cerevisiae organelles. Mol. Cell. Proteomics 2010, 9, 431-445.
29. Yates, J. R., 3rd, Gilchrist, A., Howell, K. E., Bergeron, J. J., Proteomics of organelles and large cellular structures. Nat. Rev. Mol. Cell. Biol. 2005, 6, 702-714.
30. Yan, W., Aebersold, R., Raines, E. W., Evolution of organelle-associated protein profiling. J. Proteomics 2009, 72, 4-11.
31. De Duve, C., Beaufay, H., A short history of tissue fractionation. J. Cell. Biol. 1981, 91, 293s-299s.
32. Yan, W., Hwang, D., Aebersold, R., Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins. Methods Mol. Biol. 2008, 432, 389-401.
33. America, A. H., Cordewener, J. H., Comparative LC-MS: a landscape of peaks and valleys. Proteomics 2008, 8, 731-749.
34. Zhu, W., Smith, J. W., Huang, C. M., Mass spectrometry-based label-free quantitative proteomics. J. Biomed. Biotechnol. 2010, 2010, 840518.
35. Ong, S. E., Mann, M., Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1, 252-262.
36. Gevaert, K., Impens, F., Ghesquiere, B., Van Damme, P. et al., Stable isotopic labeling in proteomics. Proteomics 2008, 8, 4873-4885.
37. Schulze, W. X., Usadel, B., Quantitation in mass-spectrometry-based proteomics. Annu. Rev. Plant. Biol. 2010, 61, 491-516.
38. Asara, J. M., Christofk, H. R., Freimark, L. M., Cantley, L. C., A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics 2008, 8, 994-999.
39. Dunkley, T. P., Watson, R., Griffin, J. L., Dupree, P., Lilley, K. S., Localization of organelle proteins by isotope tagging (LOPIT). Mol. Cell. Proteomics 2004, 3, 1128-1134.
40. Sadowski, P. G., Dunkley, T. P., Shadforth, I. P., Dupree, P. et al., Quantitative proteomic approach to study subcellular localization of membrane proteins. Nat. Protoc. 2006, 1, 1778-1789.
41. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
42. Dunkley, T. P., Hester, S., Shadforth, I. P., Runions, J. et al., Mapping the Arabidopsis organelle proteome. Proc. Natl. Acad. Sci. USA 2006, 103, 6518-6523.
43. Hall, S. L., Hester, S., Griffin, J. L., Lilley, K. S., Jackson, A. P., The organelle proteome of the DT40 lymphocyte cell line. Mol. Cell. Proteomics 2009, 8, 1295-1305.
44. Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P. et al., Proteomic characterization of the human centrosome by protein correlation profiling. Nature 2003, 426, 570-574.
45. Silva, J. C., Gorenstein, M. V., Li, G. Z., Vissers, J. P., Geromanos, S. J., Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell. Proteomics 2006, 5, 144-156.
46. Rappsilber, J., Ryder, U., Lamond, A. I., Mann, M., Large-scale proteomic analysis of the human spliceosome. Genome Res. 2002, 12, 1231-1245.
47. Ishihama, Y., Oda, Y., Tabata, T., Sato, T. et al., Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4, 1265-1272.
48. Liu, H., Sadygov, R. G., Yates, J. R., 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
49. Gilchrist, A., Au, C. E., Hiding, J., Bell, A. W. et al., Quantitative proteomics analysis of the secretory pathway. Cell 2006, 127, 1265-1281.
50. Foster, L. J., de Hoog, C. L., Zhang, Y., Xie, X. et al., A mammalian organelle map by protein correlation profiling. Cell 2006, 125, 187-199.
51. Andreyev, A. Y., Shen, Z., Guan, Z., Ryan, A. et al., Application of proteomic marker ensembles to subcellular organelle identification. Mol. Cell. Proteomics 2010, 9, 388-402.
52. Lingwood, D., Simons, K., Lipid rafts as a membrane-organizing principle. Science 2010, 327, 46-50.
53. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
54. Foster, L. J., De Hoog, C. L., Mann, M., Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc. Natl. Acad. Sci. USA 2003, 100, 5813-5818.
55. Kierszniowska, S., Seiwert, B., Schulze, W. X., Definition of Arabidopsis sterol-rich membrane microdomains by differential treatment with methyl-beta-cyclodextrin and quantitative proteomics. Mol. Cell. Proteomics 2009, 8, 612-623.
56. Brown, D. A., Lipid rafts, detergent-resistant membranes, and raft targeting signals. Physiology (Bethesda) 2006, 21, 430-439.
57. Parton, R. G., Simons, K., The multiple faces of caveolae. Nat. Rev. Mol. Cell. Biol. 2007, 8, 185-194.
58. Charrin, S., le Naour, F., Silvie, O., Milhiet, P. E. et al., Lateral organization of membrane proteins: tetraspanins spin their web. Biochem. J. 2009, 420, 133-154.
59. Lajoie, P., Goetz, J. G., Dennis, J. W., Nabi, I. R., Lattices, rafts, and scaffolds: domain regulation of receptor signaling at the plasma membrane. J. Cell. Biol. 2009, 185, 381-385.
60. Di Guglielmo, G. M., Le Roy, C., Goodfellow, A. F., Wrana, J. L., Distinct endocytic pathways regulate TGF-beta receptor signalling and turnover. Nat. Cell. Biol. 2003, 5, 410-421.
61. Murphy, J. E., Padilla, B. E., Hasdemir, B., Cottrell, G. S., Bunnett, N. W., Endosomes: a legitimate platform for the signaling train. Proc. Natl. Acad. Sci. USA 2009, 106, 17615-17622.
62. Sorkin, A., von Zastrow, M., Endocytosis and signalling: intertwining molecular networks. Nat. Rev. Mol. Cell. Biol. 2009, 10, 609-622.
63. Rogers, L. D., Foster, L. J., The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 2007, 104, 18520-18525.
64. Pertl, H., Schulze, W. X., Obermeyer, G., The pollen organelle membrane proteome reveals highly spatial-temporal dynamics during germination and tube growth of lily pollen. J. Proteome Res. 2009, 8, 5142-5152.
65. Kislinger, T., Cox, B., Kannan, A., Chung, C. et al., Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 2006, 125, 173-186.
66. 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.
67. Oh, P., Li, Y., Yu, J., Durr, E. et al., Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy. Nature 2004, 429, 629-635.
68. Boisvert, F. M., Lam, Y. W., Lamont, D., Lamond, A. I., A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage. Mol. Cell. Proteomics 2010, 9, 457-470.
69. Molina, H., Yang, Y., Ruch, T., Kim, J. W. et al., Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy. J. Proteome Res. 2009, 8, 48-58.
70. Christiano, R., Amessou, M., Shi, G., Azoulay, M. et al., Chemistry-based protein modification strategy for endocytic pathway analysis. Biol. Cell 2010, 102, 351-359.
71. Frohlich, F., Walther, T. C., Comparing cellular proteomes by mass spectrometry. Genome Biol. 2009, 10, 240.
72. Cohen, A. A., Geva-Zatorsky, N., Eden, E., Frenkel-Morgenstern, M. et al., Dynamic proteomics of individual cancer cells in response to a drug. Science 2008, 322, 1511-1516.
73. Simpson, R. J., Lim, J. W., Moritz, R. L., Mathivanan, S., Exosomes: proteomic insights and diagnostic potential. Expert Rev. Proteomics 2009, 6, 267-283.
74. Thery, C., Ostrowski, M., Segura, E., Membrane vesicles as conveyors of immune responses. Nat. Rev. Immunol. 2009, 9, 581-593.
75. Zheng, Y. Z., Foster, L. J., Contributions of quantitative proteomics to understanding membrane microdomains. J. Lipid Res. 2009, 50, 1976-1985.
76. Zech, T., Ejsing, C. S., Gaus, K., de Wet, B. et al., Accumulation of raft lipids in T-cell plasma membrane domains engaged in TCR signalling. EMBO J. 2009, 28, 466-476.
77. Pham, T. K., Wright, P. C., Proteomic analysis of Saccharomyces cerevisiae. Expert Rev. Proteomics 2007, 4, 793-813.
78. Delom, F., Szponarski, W., Sommerer, N., Boyer, J. C. et al., The plasma membrane proteome of Saccharomyces cerevisiae and its response to the antifungal calcofluor. Proteomics 2006, 6, 3029-3039.
79. de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L. et al., Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455, 1251-1254.
80. Stanislas, T., Bouyssie, D., Rossignol, M., Vesa, S. et al., Quantitative proteomics reveals a dynamic association of proteins to detergent-resistant membranes upon elicitor signaling in tobacco. Mol. Cell. Proteomics 2009, 8, 2186-2198.
81. Nouri, M. Z., Komatsu, S., Comparative analysis of soybean plasma membrane proteins under osmotic stress using gel-based and LC MS/MS-based proteomics approaches. Proteomics 2010.
82. Lin, S. L., Chien, C. W., Han, C. L., Chen, E. S. et al., Temporal proteomics profiling of lipid rafts in CCR6-activated T cells reveals the integration of actin cytoskeleton dynamics. J. Proteome Res. 2010, 9, 283-297.
83. Prokhorova, T. A., Rigbolt, K. T., Johansen, P. T., Henningsen, J. et al., Stable isotope labeling by amino acids in cell culture (SILAC) and quantitative comparison of the membrane proteomes of self-renewing and differentiating human embryonic stem cells. Mol. Cell. Proteomics 2009, 8, 959-970.
84. Conrotto, P., Roesli, C., Rybak, J., Kischel, P. et al., Identification of new accessible tumor antigens in human colon cancer by ex vivo protein biotinylation and comparative mass spectrometry analysis. Int. J. Cancer 2008, 123, 2856-2864.
85. Roesli, C., Mumprecht, V., Neri, D., Detmar, M., Identification of the surface-accessible, lineage-specific vascular proteome by two-dimensional peptide mapping. FASEB J. 2008, 22, 1933-1944.
86. Aggelis, V., Craven, R. A., Peng, J., Harnden, P. et al., Proteomic identification of differentially expressed plasma membrane proteins in renal cell carcinoma by stable isotope labelling of a von Hippel-Lindau transfectant cell line model. Proteomics 2009, 9, 2118-2130.
87. Boyd, R. S., Jukes-Jones, R., Walewska, R., Brown, D. et al., Protein profiling of plasma membranes defines aberrant signaling pathways in mantle cell lymphoma. Mol. Cell. Proteomics 2009, 8, 1501-1515.
88. Leth-Larsen, R., Lund, R., Hansen, H. V., Laenkholm, A. V. et al., Metastasis-related plasma membrane proteins of human breast cancer cells identified by comparative quantitative mass spectrometry. Mol. Cell. Proteomics 2009, 8, 1436-1449.
89. Lund, R., Leth-Larsen, R., Jensen, O. N., Ditzel, H. J., Efficient isolation and quantitative proteomic analysis of cancer cell plasma membrane proteins for identification of metastasis-associated cell surface markers. J. Proteome Res. 2009, 8, 3078-3090.
90. Roesli, C., Borgia, B., Schliemann, C., Gunthert, M. et al., Comparative analysis of the membrane proteome of closely related metastatic and nonmetastatic tumor cells. Cancer Res. 2009, 69, 5406-5414.
91. Borgia, B., Roesli, C., Fugmann, T., Schliemann, C. et al., A proteomic approach for the identification of vascular markers of liver metastasis. Cancer Res. 2010, 70, 309-318.
92. Luque-Garcia, J. L., Martinez-Torrecuadrada, J. L., Epifano, C., Canamero, M. et al., Differential protein expression on the cell surface of colorectal cancer cells associated to tumor metastasis. Proteomics 2010, 10, 940-952.
93. Schliemann, C., Roesli, C., Kamada, H., Borgia, B. et al., In vivo biotinylation of the vasculature in B-cell lymphoma identifies BST-2 as a target for antibody-based therapy. Blood 2010, 115, 736-744.
94. Wold, F., In vivo chemical modification of proteins (post-translational modification). Annu. Rev. Biochem. 1981, 50, 783-814.
95. Balan, L., Foltyn, V. N., Zehl, M., Dumin, E. et al., Feedback inactivation of D-serine synthesis by NMDA receptor-elicited translocation of serine racemase to the membrane. Proc. Natl. Acad. Sci. USA 2009, 106, 7589-7594.
96. Zhang, J., Nodzynski, T., Pencik, A., Rolcik, J., Friml, J., PIN phosphorylation is sufficient to mediate PIN polarity and direct auxin transport. Proc. Natl. Acad. Sci. USA 2010, 107, 918-922.
97. Acconcia, F., Sigismund, S., Polo, S., Ubiquitin in trafficking: the network at work. Exp. Cell Res. 2009, 315, 1610-1618.
98. Miranda, M., Sorkin, A., Regulation of receptors and transporters by ubiquitination: new insights into surprisingly similar mechanisms. Mol. Interv. 2007, 7, 157-167.
99. Sorkin, A., Goh, L. K., Endocytosis and intracellular trafficking of ErbBs. Exp. Cell Res. 2009, 315, 683-696.
100. Hor, S., Ziv, T., Admon, A., Lehner, P. J., Stable isotope labeling by amino acids in cell culture and differential plasma membrane proteome quantitation identify new substrates for the MARCH9 transmembrane E3 ligase. Mol. Cell. Proteomics 2009, 8, 1959-1971.
101. Nita-Lazar, A., Saito-Benz, H., White, F. M., Quantitative phosphoproteomics by mass spectrometry: past, present, and future. Proteomics 2008, 8, 4433-4443.
102. Kersten, B., Agrawal, G. K., Durek, P., Neigenfind, J. et al., Plant phosphoproteomics: an update. Proteomics 2009, 9, 964-988.
103. Macek, B., Mann, M., Olsen, J. V., Global and site-specific quantitative phosphoproteomics: principles and applications. Annu. Rev. Pharmacol. Toxicol. 2009, 49, 199-221.
104. Thingholm, T. E., Jensen, O. N., Larsen, M. R., Analytical strategies for phosphoproteomics. Proteomics 2009, 9, 1451-1468.
105. Tedford, N. C., Hall, A. B., Graham, J. R., Murphy, C. E. et al., Quantitative analysis of cell signaling and drug action via mass spectrometry-based systems level phosphoproteomics. Proteomics 2009, 9, 1469-1487.
106. Morandell, S., Stasyk, T., Skvortsov, S., Ascher, S., Huber, L. A., Quantitative proteomics and phosphoproteomics reveal novel insights into complexity and dynamics of the EGFR signaling network. Proteomics 2008, 8, 4383-4401.
107. Schuchardt, S., Borlak, J., Quantitative mass spectrometry to investigate epidermal growth factor receptor phosphorylation dynamics. Mass Spectrom. Rev. 2008, 27, 51-65.
108. Wisniewski, J. R., Nagaraj, N., Zougman, A., Gnad, F., Mann, M., Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology. J. Proteome Res. 2010, 9, 3280-3289.
109. Nuhse, T. S., Stensballe, A., Jensen, O. N., Peck, S. C., Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell 2004, 16, 2394-2405.
110. Benschop, J. J., Mohammed, S., O'Flaherty, M., Heck, A. J. et al., Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis. Mol. Cell. Proteomics 2007, 6, 1198-1214.
111. Niittyla, T., Fuglsang, A. T., Palmgren, M. G., Frommer, W. B., Schulze, W. X., Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis. Mol. Cell. Proteomics 2007, 6, 1711-1726.
112. Nuhse, T. S., Bottrill, A. R., Jones, A. M., Peck, S. C., Quantitative phosphoproteomic analysis of plasma membrane proteins reveals regulatory mechanisms of plant innate immune responses. Plant J. 2007, 51, 931-940.
113. Prak, S., Hem, S., Boudet, J., Viennois, G. et al., Multiple phosphorylations in the C-terminal tail of plant plasma membrane aquaporins: role in subcellular trafficking of AtPIP2;1 in response to salt stress. Mol. Cell. Proteomics 2008, 7, 1019-1030.
114. Ohtsubo, K., Marth, J. D., Glycosylation in cellular mechanisms of health and disease. Cell 2006, 126, 855-867.
115. Zaia, J., Mass spectrometry and the emerging field of glycomics. Chem. Biol. 2008, 15, 881-892.
116. Tissot, B., North, S. J., Ceroni, A., Pang, P. C. et al., Glycoproteomics: past, present and future. FEBS Lett. 2009, 583, 1728-1735.
117. Zhao, Y., Jensen, O. N., Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics 2009, 9, 4632-4641.
118. Vercoutter-Edouart, A. S., Slomianny, M. C., Dekeyzer-Beseme, O., Haeuw, J. F., Michalski, J. C., Glycoproteomics and glycomics investigation of membrane N-glycosylproteins from human colon carcinoma cells. Proteomics 2008, 8, 3236-3256.
119. Arcinas, A., Yen, T. Y., Kebebew, E., Macher, B. A., Cell surface and secreted protein profiles of human thyroid cancer cell lines reveal distinct glycoprotein patterns. J. Proteome Res. 2009, 8, 3958-3968.
120. Whelan, S. A., Lu, M., He, J., Yan, W. et al., Mass spectrometry (LC-MS/MS) site-mapping of N-glycosylated membrane proteins for breast cancer biomarkers. J. Proteome Res. 2009, 8, 4151-4160.
121. Lee, A., Chick, J. M., Kolarich, D., Haynes, P. A. et al., Liver membrane proteome glycosylation changes in mice bearing an extra-hepatic tumour. Mol. Cell. Proteomics 2010, doi: 10.1074/mcp.M900538-MCP200.
122. Doucet, A., Butler, G. S., Rodriguez, D., Prudova, A., Overall, C. M., Metadegradomics: toward in vivo quantitative degradomics of proteolytic post-translational modifications of the cancer proteome. Mol. Cell. Proteomics 2008, 7, 1925-1951.
123. Impens, F., Colaert, N., Helsens, K., Plasman, K. et al., MS-driven protease substrate degradomics. Proteomics 2010, 10, 1284-1296.
124. Doherty, M. K., Hammond, D. E., Clague, M. J., Gaskell, S. J., Beynon, R. J., Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J. Proteome Res. 2009, 8, 104-112.
125. Li, X., Jia, X., Xie, C., Lin, Y. et al., Development of cationic colloidal silica-coated magnetic nanospheres for highly selective and rapid enrichment of plasma membrane fractions for proteomics analysis. Biotechnol. Appl. Biochem. 2009, 54, 213-220.
126. Patel, V. J., Thalassinos, K., Slade, S. E., Connolly, J. B. et al., A comparison of labeling and label-free mass spectrometry-based proteomics approaches. J. Proteome Res. 2009, 8, 3752-3759.
127. Pan, S., Aebersold, R., Chen, R., Rush, J. et al., Mass spectrometry based targeted protein quantification: methods and applications. J. Proteome Res. 2009, 8, 787-797.
128. Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J. et al., Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 2009, 27, 633-641.
129. Keshishian, H., Addona, T., Burgess, M., Mani, D. R. et al., Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 2009, 8, 2339-2349.
130. Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., Aebersold, R., Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 2009, 138, 795-806.
131. Schindler, J., Nothwang, H. G., Aqueous polymer two-phase systems: effective tools for plasma membrane proteomics. Proteomics 2006, 6, 5409-5417.