Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry

Molecular and Cellular Proteomics

Volumn 11, Issue 8, 2012, Pages 342-354

  Olsson, Niclas ^a   James, Peter ^a   Borrebaeck, Carl A K ^a   Wingren, Christer ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL; FUNGAL PROTEIN; GLUCOSE; PROTEOME;

AMINO ACID ANALYSIS; ANTIBODY AFFINITY; ANTIBODY SPECIFICITY; ARTICLE; CATION EXCHANGE; CELL CULTURE; CONTROLLED STUDY; FUNCTIONAL PROTEOMICS; ISOTOPE LABELING; MASS SPECTROMETRY; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN MODIFICATION; PROTEIN MOTIF; PROTEIN TARGETING; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; SACCHAROMYCES CEREVISIAE; SENSITIVITY ANALYSIS;

AMINO ACID SEQUENCE; HUMANS; ISOTOPE LABELING; MASS SPECTROMETRY; PEPTIDES; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION;

EID: 84864827587     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M111.016238     Document Type: Article

References (51)

1. Hanash, S. (2003) Disease proteomics. Nature 422, 226-232
2. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
3. Cravatt, B. F., Simon, G. M., and Yates, J. R., 3rd (2007) The biological impact of mass-spectrometry-based proteomics. Nature 450, 991-1000
4. Bengtsson, S., Krogh, M., Szigyarto, C. A., Uhlen, M., Schedvins, K., Silfverswärd, C., Linder, S., Auer, G., Alaiya, A., and James, P. (2007) Large-scale proteomics analysis of human ovarian cancer for biomarkers. J. Proteome Res. 6, 1440-1450
5. Whiteaker, J. R., Lin, C., Kennedy, J., Hou, L., Trute, M., Sokal, I., Yan, P., Schoenherr, R. M., Zhao, L., Voytovich, U. J., Kelly-Spratt, K. S., Krasnoselsky, A., Gafken, P. R., Hogan, J. M., Jones, L. A., Wang, P., Amon, L., Chodosh, L. A., Nelson, P. S., McIntosh, M. W., Kemp, C. J., and Paulovich, A. G. (2011) A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotechnol. 29, 625-634
6. Listgarten, J., and Emili, A. (2005) Practical proteomic biomarker discovery: taking a step back to leap forward. Drug Discov. Today 10, 1697-1702
7. Borrebaeck, C. A., and Wingren, C. (2007) High-throughput proteomics using antibody microarrays: an update. Expert Rev. Mol. Diagn. 7, 673-686
8. Borrebaeck, C. A., and Wingren, C. (2009) Design of high-density antibody microarrays for disease proteomics: key technological issues. J. Proteomics 72, 928-935
9. Haab, B. B. (2006) Applications of antibody array platforms. Curr. Opin. Biotechnol. 17, 415-421
10. Kingsmore, S. F. (2006) Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat. Rev. Drug Discov. 5, 310-320
11. Ayoglu, B., Häggmark, A., Neiman, M., Igel, U., Uhlén, M., Schwenk, J. M., and Nilsson, P. (2011) Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev. Mol. Diagn. 11, 219-234
12. Carlsson, A., Wingren, C., Kristensson, M., Rose, C., Fernö, M., Olsson, H., Jernstrom, H., Ek, S., Gustavsson, E., Ingvar, C., Ohlsson, M., Peterson, C., and Borrebaeck, C. A. K. (2011) Molecular serum portraits in patients with primary breast cancer predict the development of distant metastases. Proc. Natl. Acad. Sci. U.S.A. 108, 14252-14257
13. Carlsson, A., Wuttge, D. M., Ingvarsson, J., Bengtsson, A. A., Sturfelt, G., Borrebaeck, C. A. K., and Wingren, C. (2011) Serum protein profiling of systemic lupus erythematosus and systemic sclerosis using recombinant antibody microarrays. Mol. Cell. Proteomics 10, M110.005033
14. Sanchez-Carbayo, M., Socci, N. D., Lozano, J. J., Haab, B. B., and Cordon- Cardo, C. (2006) Profiling bladder cancer using targeted antibody arrays. Am. J. Pathol. 168, 93-103
15. Dexlin-Mellby, L., Sandström, A., Centlow, M., Nygren, S., Hansson, S. R., Borrebaeck, C. A. K., and Wingren, C. (2010) Tissue proteome profiling of preeclamptic placenta using recombinant antibody microarrays. Proteomics Clin. Appl. 4, 794-807
16. Borrebaeck, C. A., and Wingren, C. (2009) Transferring proteomic discoveries into clinical practice. Expert Rev. Proteomics 6, 11-13
17. 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
18. 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
19. 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
20. 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
21. Hoeppe, S., Schreiber, T. D., Planatscher, H., Zell, A., Templin, M. F., Stoll, D., Joos, T. O., and Poetz, O. (2011) Targeting Peptide termini, a novel immunoaffinity approach to reduce complexity in mass spectrometric protein identification. Mol. Cell. Proteomics 10, M110.002857
22. Olsson, N., Wingren, C., Mattsson, M., James, P., O'Connell, D., Nilsson, F., Cahill, D. J., and Borrebaeck, C. A. K. (2011) Proteomic analysis and discovery using affinity proteomics and mass spectrometry. Mol. Cell. Proteomics 10, M110.003962
23. Wingren, C., and Borrebaeck, C. A. K. (2009) Antibody-based microarrays. Methods Mol. Biol. 509, 57-84
24. Söderlind, E., Strandberg, L., Jirholt, P., Kobayashi, N., Alexeiva, V., Aberg, A. M., Nilsson, A., Jansson, B., Ohlin, M., Wingren, C., Danielsson, L., Carlsson, R., and Borrebaeck, C. A. (2000) Recombining germline-derived CDR sequences for creating diverse single-framework antibody libraries. Nat. Biotechnol. 18, 852-856
25. 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 for Mol. Biol. 5, 28
26. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386
27. Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P., Faergeman, N. J., Mann, M., and Jensen, O. N. (2005) Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 4, 310-327
28. Grassl, J., Westbrook, J. A., Robinson, A., Borén, M., Dunn, M. J., and Clyne, R. K. (2009) Preserving the yeast proteome from sample degradation. Proteomics 9, 4616-4626
29. Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372
30. Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. (2004) WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190
31. Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P., and von Mering, C. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37, D412-416
32. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425, 737-741
33. 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 spectrometry: SILAC labeled yeast as a model system. Genome Biol. 7, R50
34. Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., and Aebersold, R. (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795-806
35. Lange, V., Malmström, J. A., Didion, J., King, N. L., Johansson, B. P., Schäfer, J., Rameseder, J., Wong, C. H., Deutsch, E. W., Brusniak, M. Y., Bühlmann, P., Bjorck, L., Domon, B., and Aebersold, R. (2008) Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol. Cell. Proteomics 7, 1489-1500
36. Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A. J., Keshishian, H., Hall, S. C., Allen, S., Blackman, R. K., Borchers, C. H., Buck, C., Cardasis, H. L., Cusack, M. P., Dodder, N. G., Gibson, B. W., Held, J. M., Hiltke, T., Jackson, A., Johansen, E. B., Kinsinger, C. R., Li, J., Mesri, M., Neubert, T. A., Niles, R. K., Pulsipher, T. C., Ransohoff, D., Rodriguez, H., Rudnick, P. A., Smith, D., Tabb, D. L., Tegeler, T. J., Variyath, A. M., Vega-Montoto, L. J., Wahlander, A., Waldemarson, S., Wang, M., Whiteaker, J. R., Zhao, L., Anderson, N. L., Fisher, S. J., Liebler, D. C., Paulovich, A. G., Regnier, F. E., Tempst, P., and Carr, S. A. (2009) Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27, 633-641
37. Picotti, P., Rinner, O., Stallmach, R., Dautel, F., Farrah, T., Domon, B., Wenschuh, H., and Aebersold, R. (2010) High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 7, 43-46
38. 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
39. Tabb, D. L., Vega-Montoto, L., Rudnick, P. A., Variyath, A. M., Ham, A. J., Bunk, D. M., Kilpatrick, L. E., Billheimer, D. D., Blackman, R. K., Cardasis, H. L., Carr, S. A., Clauser, K. R., Jaffe, J. D., Kowalski, K. A., Neubert, T. A., Regnier, F. E., Schilling, B., Tegeler, T. J., Wang, M., Wang, P., Whiteaker, J. R., Zimmerman, L. J., Fisher, S. J., Gibson, B. W., Kinsinger, C. R., Mesri, M., Rodriguez, H., Stein, S. E., Tempst, P., Paulovich, A. G., Liebler, D. C., and Spiegelman, C. (2010) Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J. Proteome Res. 9, 761-776
40. Swaney, D. L., Wenger, C. D., and Coon, J. J. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J. Proteome Res. 9, 1323-1329
41. Gan, C. S., Chong, P. K., Pham, T. K., and Wright, P. C. (2007) Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ). J. Proteome Res. 6, 821-827
42. de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., and Mann, M. (2008) Comprehensive mass-spectrometry- based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254
43. Kolkman, A., Olsthoorn, M. M., Heeremans, C. E., Heck, A. J., and Slijper, M. (2005) Comparative proteome analysis of Saccharomyces cerevisiae grown in chemostat cultures limited for glucose or ethanol. Mol. Cell. Proteomics 4, 1-11
44. Zaman, S., Lippman, S. I., Zhao, X., and Broach, J. R. (2008) How Saccharomyces responds to nutrients. Annu. Rev. Genet. 42, 27-81
45. Hung, G. C., Brown, C. R., Wolfe, A. B., Liu, J., and Chiang, H. L. (2004) Degradation of the gluconeogenic enzymes fructose-1,6-bisphosphatase and malate dehydrogenase is mediated by distinct proteolytic pathways and signaling events. J. Biol. Chem. 279, 49138-49150
46. Santt, O., Pfirrmann, T., Braun, B., Juretschke, J., Kimmig, P., Scheel, H., Hofmann, K., Thumm, M., and Wolf, D. H. (2008) The yeast GID complex, a novel ubiquitin ligase (E3) involved in the regulation of carbohydrate metabolism. Mol. Biol. Cell 19, 3323-3333
47. Costenoble, R., Picotti, P., Reiter, L., Stallmach, R., Heinemann, M., Sauer, U., and Aebersold, R. (2011) Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Mol. Syst. Biol. 7, 464
48. Lee, M. V., Topper, S. E., Hubler, S. L., Hose, J., Wenger, C. D., Coon, J. J., and Gasch, A. P. (2011) A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol. Syst. Biol. 7, 514
49. Alexandre, H., Ansanay-Galeote, V., Dequin, S., and Blondin, B. (2001) Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Lett. 498, 98-103
50. Pleiss, J. A., Whitworth, G. B., Bergkessel, M., and Guthrie, C. (2007) Rapid, transcript-specific changes in splicing in response to environmental stress. Mol. Cell. 27, 928-937
51. Dinh, T. N., Nagahisa, K., Yoshikawa, K., Hirasawa, T., Furusawa, C., and Shimizu, H. (2009) Analysis of adaptation to high ethanol concentration in Saccharomyces cerevisiae using DNA microarray. Bioprocess. Biosyst. Eng. 32, 681-688