Targeting peptide termini, a novel immunoaffinity approach to reduce complexity in mass spectrometric protein identification

Molecular and Cellular Proteomics

Volumn 10, Issue 2, 2011, Pages

  Hoeppe, Sibylle ^a   Schreiber, Thomas D ^a   Planatscher, Hannes ^b   Zell, Andreas ^b   Templin, Markus F ^a   Stoll, Dieter ^a,c   Joos, Thomas O ^a   Poetz, Oliver ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b UNIVERSITY OF TÜBINGEN   (Germany)

^c ALBSTADT SIGMARINGEN UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; EPITOPE; PROTEIN ANTIBODY; TRYPSIN; ANTIBODY; PEPTIDE; PROTEIN; PROTEOME;

AMINO ACID SEQUENCE; ANTIBODY SPECIFICITY; ARTICLE; CARBOXY TERMINAL SEQUENCE; CELL LYSATE; CONTROLLED STUDY; HUMAN; HUMAN CELL; IMMUNOAFFINITY CHROMATOGRAPHY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN TARGETING; SENSITIVITY ANALYSIS; TANDEM MASS SPECTROMETRY; CELL LINE; CELL STRAIN HEK293; CHEMISTRY; GENE LIBRARY; MASS SPECTROMETRY; METHODOLOGY; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; PROTEOMICS;

ANTIBODIES; CELL LINE; EPITOPES; GENE LIBRARY; HEK293 CELLS; HUMANS; MASS SPECTROMETRY; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOME; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRYPSIN;

EID: 79953205955     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M110.002857     Document Type: Article

References (34)

1. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207 (Pubitemid 36362757)
2. 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
3. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247
4. Bodovitz, S., and Patterson, S. (2003) Protein biomarker strategies. Drug Discov. World Fall, 67-78
5. Anderson, L., and Hunter, C. L. (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 5, 573-588
6. Keshishian, H., Addona, T., Burgess, M., Kuhn, E., and Carr, S. A. (2007) Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 6, 2212-2229
7. Fang, X., and Zhang, W. W. (2008) Affinity separation and enrichment methods in proteomic analysis. J. Proteomics 71, 284-303
8. Pernemalm, M., Lewensohn, R., and Lehtiö, J. (2009) Affinity prefractionation for MS-based plasma proteomics. Proteomics 9, 1420-1427
9. Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W., and Pearson, T. W. (2004) Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J. Proteome Res. 3, 235-244
10. Whiteaker, J. R., Zhao, L., Zhang, H. Y., Feng, L. C., Piening, B. D., Anderson, L., and Paulovich, A. G. (2007) Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Anal. Biochem. 362, 44-54
11. Whiteaker, J. R., Zhao, L., Anderson, L., and Paulovich, A. G. (2010) An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol. Cell. Proteomics 9, 184-196
12. Anderson, N. L., Anderson, N. G., Pearson, T. W., Borchers, C. H., Paulovich, A. G., Patterson, S. D., Gillette, M., Aebersold, R., and Carr, S. A. (2009) A human proteome detection and quantitation project. Mol. Cell. Proteomics 8, 883-886
13. Schmelzle, K., and White, F. M. (2006) Phosphoproteomic approaches to elucidate cellular signaling networks. Curr. Opin. Biotechnol. 17, 406-414
14. Steen, H., Kuster, B., Fernandez, M., Pandey, A., and Mann, M. (2002) Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J. Biol. Chem. 277, 1031-1039
15. Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., and Mann, M. (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834-840
16. Kim, S. C., Sprung, R., Chen, Y., Xu, Y., Ball, H., Pei, J., Cheng, T., Kho, Y., Xiao, H., Xiao, L., Grishin, N. V., White, M., Yang, X. J., and Zhao, Y. (2006) Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol. Cell 23, 607-618 (Pubitemid 44205490)
17. Rush, J., Moritz, A., Lee, K. A., Guo, A., Goss, V. L., Spek, E. J., Zhang, H., Zha, X. M., Polakiewicz, R. D., and Comb, M. J. (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol. 23, 94-101
18. Poetz, O., Hoeppe, S., Templin, M. F., Stoll, D., and Joos, T. O. (2009) Proteome wide screening using peptide affinity capture. Proteomics 9, 1518-1523
19. Wingren, C., James, P., and Borrebaeck, C. A. K. (2009) Strategy for surveying the proteome using affinity proteomics and mass spectrometry. Proteomics 9, 1511-1517
20. Poetz, O., Ostendorp, R., Brocks, B., Schwenk, J. M., Stoll, D., Joos, T. O., and Templin, M. F. (2005) Protein microarrays for antibody profiling: Specificity and affinity determination on a chip. Proteomics 5, 2402-2411
21. Kurzeder, C., Koppold, B., Sauer, G., Pabst, S., Kreienberg, R., and Deissler, H. (2007) CD9 promotes adeno-associated virus type 2 infection of mammary carcinoma cells with low cell surface expression of heparan sulphate proteoglycans. Int. J. Mol. Med. 19, 325-333
22. Anderson, N. L., Haines, L. R., and Pearson, T. W. (2004) An effective and rapid method for functional characterization of immunoadsorbents using POROS beads and flow cytometry. J. Proteome Res. 3, 228-234
23. Behrens, J., and Lustig, B. (2004) The Wnt connection to tumorigenesis. Int. J. Dev. Biol. 48, 477-487
24. Dihlmann, S., and von Knebel Doeberitz, M. (2005) Wnt/beta-catenin- pathway as a molecular target for future anti-cancer therapeutics. Int. J. Cancer 113, 515-524 (Pubitemid 40038726)
25. MacDonald, B. T., Tamai, K., and He, X. (2009) Wnt/beta-catenin signaling: components, mechanisms, and diseases. Dev. Cell 17, 9-26
26. Henderson, G., and Bradley, M. (2007) Functional peptide arrays for high-throughput chemical biology based applications. Curr. Opin. Biotechnol. 18, 326-330
27. Coghlan, M. P., Culbert, A. A., Cross, D. A., Corcoran, S. L., Yates, J. W., Pearce, N. J., Rausch, O. L., Murphy, G. J., Carter, P. S., Roxbee Cox, L., Mills, D., Brown, M. J., Haigh, D., Ward, R. W., Smith, D. G., Murray, K. J., Reith, A. D., and Holder, J. C. (2000) Selective small molecule inhibitors of glycogen synthase kinase-3 modulate glycogen metabolism and gene transcription. Chem. Biol. 7, 793-803
28. Liu, C., Li, Y., Semenov, M., Han, C., Baeg, G. H., Tan, Y., Zhang, Z., Lin, X., and He, X. (2002) Control of beta-catenin phosphorylation/degradation by a dual-kinase mechanism. Cell 108, 837-847 (Pubitemid 34327534)
29. Jiang, J., Parker, C. E., Hoadley, K. A., Perou, C. M., Boysen, G., and Borchers, C. H. (2007) Development of an immuno tandem mass spectrometry (iMALDI) assay for EGFR diagnosis. Proteomics Clin. Appl. 1, 1651-1659
30. Beavis, R. C. (2006) Using the global proteome machine for protein identification. Methods Mol. Biol. 328, 217-228
31. Deutsch, E. W. (2010) The PeptideAtlas Project. Methods Mol. Biol. 604, 285-296
32. Deutsch, E. W., Lam, H., and Aebersold, R. (2008) PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9, 429-434 (Pubitemid 351627279)
33. Planatscher, H., Supper, J., Poetz, O., Stoll, D., Joos, T., Templin, M. F., and Zell, A. (2010) Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry. Algorithms Mol. Biol. 5, 28
34. McCrea, P. D., and Gu, D. (2010) The catenin family at a glance. J. Cell. Sci. 123, 637-642