Quantitative analysis of protein phosphorylation on A system-wide scale by mass spectrometry-based proteomics

Methods in Enzymology

Volumn 470, Issue C, 2010, Pages 317-334

  Bodenmiller, Bernd ^a,d   Aebersold, Ruedi ^a,b,c  

^a ETH ZURICH   (Switzerland)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^c UNIVERSITY OF ZURICH   (Switzerland)

^d STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DENDRIMER; PEPTIDE; PHOSPHATASE; PHOSPHOPEPTIDE; PHOSPHORAMIDIC ACID; PHOSPHORAMIDIC ACID DERIVATIVE; PHOSPHOTRANSFERASE; PROTEIN KINASE; RESIN; TITANIUM DIOXIDE; TRICHLOROACETIC ACID;

AMINO ACID SEQUENCE; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; CULTURE MEDIUM; CYTOLYSIS; DATA ANALYSIS; DATA BASE; DELETION MUTANT; ENZYME ACTIVITY; ENZYME SUBSTRATE; EUKARYOTIC CELL; FUNGAL STRAIN; GENE DELETION; IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY; IN VIVO STUDY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PH; PRIORITY JOURNAL; PROTEIN ISOLATION; PROTEIN PHOSPHORYLATION; PROTEIN PURIFICATION; PROTEOMICS; QUANTITATIVE ANALYSIS; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TIME OF FLIGHT MASS SPECTROMETRY; WILD TYPE; YEAST CELL;

EUKARYOTA;

EID: 77956028057     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)70013-6     Document Type: Article

References (40)

1. Aebersold, R., andGoodlett, D. R. (2001). Mass spectrometry in proteomics. Chem. Rev. 101, 269-295.
2. Aebersold, R., andMann, M. (2003). Mass spectrometry-based proteomics. Nature 422, 198-207.
3. Andersson, L., andPorath, J. (1986). Isolation of phosphoproteins by immobilized metal (Fe3) affinity-chromatography. Anal. Biochem. 154, 250-254.
4. Bakalarski, C. E., Haas, W., Dephoure, N. E., andGygi, S. P. (2007). The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics. Anal. Bioanal. Chem. 389, 1409-1419.
5. Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E., Villen, J., Li, J. X., Cohn, M. A., Cantley, L. C., andGygi, S. P. (2004). Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. USA 101, 12130-12135.
6. Benjamini, Y., andHochberg, Y. (1995). Controlling the false discovery rate-A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B-Methodological 57, 289-300.
7. 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., et al. (2007a). PhosphoPep-A phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol. Syst. Biol. 3, 139.
8. Bodenmiller, B., Mueller, L. N., Mueller, M., Domon, B., andAebersold, R. (2007b). Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat. Methods 4, 231-237. (Pubitemid 46358873)
9. Bodenmiller, B., Mueller, L. N., Pedrioli, P. G., Pflieger, D., Junger, M. A., Eng, J. K., Aebersold, R., andTao, W. A. (2007c). An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: Application to Drosophila melanogaster Kc167 cells. Mol. Biosyst. 3, 275-286.
10. Bodenmiller, B., Wanka, S., Kraft, C., Urbano, J., Campbell, D., Gerrits, B., Picotti, P., Lam, H., Vitek, O., Brusniak, M. Y., Schlapbach, R., Shokat, K., et al. (submitted). An In Vivo Protein Phosphorylation Network of Budding Yeast.
11. Brusniak, M. Y., Bodenmiller, B., Campbell, D., Cooke, K., Eddes, J., Garbutt, A., Lau, H., Letarte, S., Mueller, L. N., Sharma, V., Vitek, O., Zhang, N., et al. (2008). Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics 9, 542.
12. Elias, J. E., andGygi, S. P. (2007). Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214.
13. Eng, J. K., McCormack, A. L., andYates, J. R. (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.
14. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J., Ross, M. M., Shabanowitz, J., Hunt, D. F., andWhite, F. M. (2002). Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20, 301-305.
15. Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P., Faergeman, N. J., Mann, M., andJensen, O. N. (2005). Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 4, 310-327.
16. He, T., Alving, K., Feild, B., Norton, J., Joseloff, E. G., Patterson, S. D., and Domon, B. (2004). Quantitation of phosphopeptides using affinity chromatography and stable isotope labeling. J. Am. Soc. Mass Spectrom. 15, 363-373.
17. Huber, A., Bodenmiller, B., Uotila, A., Stahl, M., Wanka, S., Gerrits, B., Aebersold, R., andLoewith, R. (2009). Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev. 23, 1929-1943.
18. Hunter, T. (2000). Signaling-2000 and beyond. Cell 100, 113-127.
19. Hunter, T., andPlowman, G. D. (1997). The protein kinases of budding yeast: Six score and more. Trends Biochem. Sci. 22, 18-22.
20. Keller, A., Nesvizhskii, A. I., Kolker, E., andAebersold, R. (2002). Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392.
21. Keller, A., Eng, J., Zhang, N., Li, X. J., andAebersold, R. (2005). A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 1(2005), 0017.
22. Larsen, M. R., Thingholm, T. E., Jensen, O. N., Roepstorff, P., andJorgensen, T. J. (2005). Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell. Proteomics 4, 873-886.
23. Macek, B., Mann, M., andOlsen, J. V. (2009). Global and site-specific quantitative phosphoproteomics: Principles and applications. Annu. Rev. Pharmacol. Toxicol. 49, 199-221.
24. Molina, H., Horn, D. M., Tang, N., Mathivanan, S., andPandey, A. (2007). Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 104, 2199-2204.
25. Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S., Bodenmiller, B., Brusniak, M. Y., Vitek, O., Aebersold, R., andMuller, M. (2007). SuperHirn-A novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7, 3470-3480. (Pubitemid 47597670)
26. Mueller, L. N., Brusniak, M. Y., Mani, D. R., andAebersold, R. (2008). An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 7, 51-61.
27. Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., andMann, M. (2006). Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635-648. (Pubitemid 44647421)
28. Perkins, D. N., Pappin, D. J., Creasy, D. M., andCottrell, J. S. (1999). Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567.
29. Pinkse, M. W. H., Uitto, P. M., Hilhorst, M. J., Ooms, B., andHeck, A. J. R. (2004). Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-nanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem. 76, 3935-3943.
30. Ptacek, J., Devgan, G., Michaud, G., Zhu, H., Zhu, X., Fasolo, J., Guo, H., Jona, G., Breitkreutz, A., Sopko, R., McCartney, R. R., Schmidt, M. C., et al. (2005). Global analysis of protein phosphorylation in yeast. Nature 438, 679-684. (Pubitemid 41740579)
31. Rinner, O., Mueller, L. N., Hubalek, M., Muller, M., Gstaiger, M., andAebersold, R. (2007). An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat. Biotechnol. 25, 345-352.
32. Salih, E. (2004). Phosphoproteomics by mass spectrometry and classical protein chemistry approaches. Mass Spectrom. Rev. 2005, Nov-Dec, 24(6), 828-846. Review.
33. Schroeder, M. J., Shabanowitz, J., Schwartz, J. C., Hunt, D. F., andCoon, J. J. (2004). A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Anal. Chem. 76, 3590-3598.
34. Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., andHunt, D. F. (2004). Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 101, 9528-9533.
35. Tan, C. S., Bodenmiller, B., Pasculescu, A., Jovanovic, M., Hengartner, M. O., Jorgensen, C., Bader, G. D., Aebersold, R., Pawson, T., andLinding, R. (2009). Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci. Signal. 2, ra39.
36. Tao, W. A., Wollscheid, B., O'Brien, R., Eng, J. K., Li, X. J., Bodenmiller, B., Watts, J. D., Hood, L., andAebersold, R. (2005). Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat. Methods 2, 591-598. (Pubitemid 41086850)
37. Thingholm, T. E., Jensen, O. N., Robinson, P. J., andLarsen, M. R. (2008). SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol. Cell. Proteomics 7, 661-671.
38. Thingholm, T. E., Jensen, O. N., andLarsen, M. R. (2009). Enrichment and separation of mono- and multiply phosphorylated peptides using sequential elution from IMAC prior to mass spectrometric analysis. Methods Mol. Biol. 527, 67-78, xi.
39. Urban, J., Soulard, A., Huber, A., Lippman, S., Mukhopadhyay, D., Deloche, O., Wanke, V., Anrather, D., Ammerer, G., Riezman, H., Broach, J. R., De Virgilio, C., et al. (2007). Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol. Cell 26, 663-674.
40. Zhou, H. L., Watts, J. D., andAebersold, R. (2001). A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19, 375-378.