Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry

Molecular and Cellular Proteomics

Volumn 8, Issue 4, 2009, Pages 624-638

  Schiess, Ralph ^a,b,c   Mueller, Lukas N ^a,c   Schmidt, Alexander ^a,c   Mueller, Markus ^d   Wollscheid, Bernd ^a,b   Aebersold, Ruedi ^a,b,c,e  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c Competence Center for Systems Physiology and Metabolic Disease ^*  (Switzerland)

^d SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^e INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DROSOPHILA PROTEIN; GLYCOPROTEIN; INSULIN; INSULIN RECEPTOR; PROTEOME;

ANIMAL; ARTICLE; CELL LINE; CELL MEMBRANE; CYTOLOGY; DROSOPHILA MELANOGASTER; DRUG EFFECT; ENDOCYTOSIS; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; REPRODUCIBILITY;

ANIMALS; CELL LINE; CELL MEMBRANE; CHROMATOGRAPHY, LIQUID; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; ENDOCYTOSIS; GLYCOPROTEINS; INSULIN; ISOTOPE LABELING; MASS SPECTROMETRY; PROTEOME; RECEPTOR, INSULIN; REPRODUCIBILITY OF RESULTS;

EID: 66149125323     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M800172-MCP200     Document Type: Article

References (43)

1. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
2. de Godoy, L. M., Olsen, J. V., de Souza, G. A., Li, G., Mortensen, P., and Mann, M. (2006) Status of complete proteome analysis by mass spec-trometry: SILAC labeled yeast as a model system. Genome Biol. 7, R50
3. Schmidt, A., Gehlenborg, N., Bodenmiller, B., Mueller, L. N., Campbell, D., Mueller, M., Aebersold, R., and Domon, B. (2008) An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol. Cell. Proteomics 7, 2138-2150
4. Mueller, L. N., Brusniak, M. Y., Mani, D. R., and Aebersold, R. (2008) An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 7, 51-61
5. Zhang, H., Yi, E. C., Li, X. J., Mallick, P., Kelly-Spratt, K. S., Masselon, C. D., Camp, D. G., II, Smith, R. D., Kemp, C. J., and Aebersold, R. (2005) High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol. Cell. Pro-teomics 4, 144-155
6. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999
7. Bodenmiller, B., Mueller, L. N., Mueller, M., Domon, B., and Aebersold, R. (2007) Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat. Methods 4, 231-237
8. Zhang, H., Li, X. J., Martin, D. B., and Aebersold, R. (2003) Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21, 660-666
9. McDonald, L., Robertson, D. H., Hurst, J. L., and Beynon, R. J. (2005) Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nat. Methods 2, 955-957
10. Marelli, M., Nesvizhskii, A. I., and Aitchison, J. D. (2008) Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions: an example in peroxisomes. Methods Mol. Biol. 432, 357-371
11. Kislinger, T., Cox, B., Kannan, A., Chung, C., Hu, P., Ignatchenko, A., Scott, M. S., Gramolini, A. O., Morris, Q., Hallett, M. T., Rossant, J., Hughes, T. R., Frey, B., and Emili, A. (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125, 173-186
12. Zola, H., Swart, B., Nicholson, I., Aasted, B., Bensussan, A., Boumsell, L., Buckley, C., Clark, G., Drbal, K., Engel, P., Hart, D., Horejsi, V., Isacke, C., Macardle, P., Malavasi, F., Mason, D., Olive, D., Saalmueller, A., Schlossman, S. F., Schwartz-Albiez, R., Simmons, P., Tedder, T. F., Uguccioni, M., and Warren, H. (2005) CD molecules 2005: human cell differentiation molecules. Blood 106, 3123-3126
13. Brunner, E., Ahrens, C. H., Mohanty, S., Baetschmann, H., Loevenich, S., Potthast, F., Deutsch, E. W., Panse, C., de Lichtenberg, U., Rinner, O., Lee, H., Pedrioli, P. G., Malmstrom, J., Koehler, K., Schrimpf, S., Krijgs-veld, J., Kregenow, F., Heck, A. J., Hafen, E., Schlapbach, R., and Aebersold, R. (2007) A high-quality catalog of the Drosophila melano-gaster proteome. Nat. Biotechnol. 25, 576-583
14. Bodenmiller, B., Malmstrom, J., Gerrits, B., Campbell, D., Lam, H., Schmidt, A., Rinner, O., Mueller, L. N., Shannon, P. T., Pedrioli, P. G., Panse, C., Lee, H. K., Schlapbach, R., and Aebersold, R. (2007) Phos-phoPep- A phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol. Syst. Biol. 3, 139
15. Rinner, O., Mueller, L. N., Hubalek, M., Muller, M., Gstaiger, M., and Aebersold, R. (2007) An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat. Biotechnol. 25, 345-352
16. Gygi, S. P., Corthals, G. L., Zhang, Y., Rochon, Y., and Aebersold, R. (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. U. S. A. 97, 9390-9395
17. Knutson, V. P., Ronnett, G. V., and Lane, M. D. (1982) Control of insulin receptor level in 3T3 cells: effect of insulin-induced down-regulation and dexamethasone-induced up-regulation on rate of receptor inactivation. Proc. Natl. Acad. Sci. U. S. A. 79, 2822-2826
18. Gahmberg, C. G., and Tolvanen, M. (1996) Why mammalian cell surface proteins are glycoproteins. Trends Biochem. Sci. 21, 308-311
19. Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S., Bodenmiller, B., Brusniak, M. Y., Vitek, O., Aebersold, R., and Muller, M. (2007) Super-Hirn- A novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7, 3470-3480
20. Arsenis, G., Hayes, G. R., and Livingston, J. N. (1985) Insulin receptor cycling and insulin action in the rat adipocyte. J. Biol. Chem. 260, 2202-2207
21. Radimerski, T., Mini, T., Schneider, U., Wettenhall, R. E., Thomas, G., and Jeno, P. (2000) Identification of insulin-induced sites of ribosomal protein S6 phosphorylation in Drosophila melanogaster. Biochemistry 39, 5766-5774
22. Schmidt, A., Kellermann, J., and Lottspeich, F. (2005) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5, 4-15
23. Pedrioli, P. G., Eng, J. K., Hubley, R., Vogelzang, M., Deutsch, E. W., Raught, B., Pratt, B., Nilsson, E., Angeletti, R. H., Apweiler, R., Cheung, K., Costello, C. E., Hermjakob, H., Huang, S., Julian, R. K., Kapp, E., McComb, M. E., Oliver, S. G., Omenn, G., Paton, N. W., Simpson, R., Smith, R., Taylor, C. F., Zhu, W., and Aebersold, R. (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22, 1459-1466
24. Eng, J., McCormack, A. L., and Yates, J. R., III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
25. Keller, A., Eng, J., Zhang, N., Li, X. J., and Aebersold, R. (2005) A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 1, 2005.0017
26. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392
27. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658
28. Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951
29. Hirokawa, T., Boon-Chieng, S., and Mitaku, S. (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14, 378-379
30. Sonnhammer, E. L., von Heijne, G., and Krogh, A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6, 175-182
31. Al-Shahrour, F., Minguez, P., Vaquerizas, J. M., Conde, L., and Dopazo, J. (2005) BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res. 33, W460-W464
32. Stanasila, L, Pattus, F., and Massotte, D. (1998) Heterologous expression of G-protein-coupled receptors: human opioid receptors under scrutiny. Biochimie (Paris) 80, 563-571
33. Wang, G., Wu, W. W., Zeng, W., Chou, C. L, and Shen, R. F. (2006) Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: reproducibility, linearity, and application with complex proteomes. J Proteome Res. 5, 1214-1223
34. Chen, W., White, M. A., and Cobb, M. H. (2002) Stimulus-specific requirements for MAP3 kinases in activating the JNK pathway. J. Biol. Chem. 277, 49105-49110
35. Botella, J. A., Baines, I. A., Williams, D. D., Goberdhan, D. C, Proud, C. G., and Wilson, C. (2001) The Drosophila cell shape regulator c-Jun N-terminal kinase also functions as a stress-activated protein kinase. Insect Biochem. Mol. Biol. 31, 839-847
36. Standaert, M. L, and Pollet, R. J. (1984) Equilibrium model for insulin-induced receptor down-regulation. Regulation of insulin receptors in differentiated BC3H-1 myocytes. J. Biol. Chem. 259, 2346-2354
37. Radimerski, T., Montagne, J., Rintelen, F., Stocker, H., van der Kaay, J., Downes, C. P., Hafen, E., and Thomas, G. (2002) dS6K-regulated cell growth is dPKB/dPI(3)K-independent, but requires dPDK1. Nat. Cell Biol. 4, 251-255
38. Kolodziej, P. A., Timpe, L. C, Mitchell, K. J., Fried, S. R., Goodman, C. S., Jan, L. Y., and Jan, Y. N. (1996) frazzled encodes a Drosophila member of the DCC immunoglobulin subfamily and is required for CNSand motor axon guidance. Cell 87, 197-204
39. Burgess, J. W., Wada, I., Ling, N., Khan, M. N., Bergeron, J. J., and Posner, B. I. (1992) Decrease in/3-subunit phosphotyrosine correlates with internalization and activation of the endosomal insulin receptor kinase. J. Biol. Chem. 267, 10077-10086
40. Authier, F., Rachubinski, R. A., Posner, B. I., and Bergeron, J. J. (1994) Endosomal proteolysis of insulin by an acidic thiol metalloprotease unrelated to insulin degrading enzyme. J. Biol. Chem. 269, 3010-3016
41. Doherty, J. J., II, Kay, D. G., Lai, W. H., Posner, B. I., and Bergeron, J. J. (1990) Selective degradation of insulin within rat liver endosomes. J. Cell Biol. 110, 35-42
42. Tomiya, N., Narang, S., Lee, Y. C, and Betenbaugh, M. J. (2004) Comparing N-glycan processing in mammalian cell lines to native and engineered lepidopteran insect cell lines. Glycoconj. J. 21, 343-360
43. Medzihradszky, K. F. (2008) Characterization of site-specific N-glycosylation. Methods Mol. Biol. 446, 293-316