Quantitative phosphoproteomics by mass spectrometry: Past, present, and future

Proteomics

Volumn 8, Issue 21, 2008, Pages 4433-4443

  Nita Lazar, Aleksandra ^a   Saito Benz, Hideshiro ^a   White, Forest M ^a,b  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Electrospray ionization tandem mass spectrometry; Protein phosphorylation; Signal transduction profiling; Spectrometry

Indexed keywords

MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEOMICS; REVIEW; SYSTEMS BIOLOGY;

ANIMALS; DRUG DISCOVERY; FORECASTING; HUMANS; MASS SPECTROMETRY; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEOMICS; RECEPTOR, EPIDERMAL GROWTH FACTOR; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 55849118087     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800231     Document Type: Review

References (60)

1. Hunter, T., Signaling-2000 and beyond. Cell 2000, 100, 113-127.
2. Seet, B. T., Dikic, I., Zhou, M. M., Pawson, T., Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol. 2006, 7, 473-483.
3. Huang, P. H., Cavenee, W. K., Furnari, F. B., White, F. M., Uncovering therapeutic targets for glioblastoma: A systems biology approach. Cell Cycle 2007, 6, 2750-2754.
4. Pawson, T., Linding, R., Network medicine. FEBS Lett. 2008.
5. Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R. et al., Analysis of receptor signaling pathways by mass spectrometry: Identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc. Natl. Acad. Sci. USA 2000, 97, 179-184.
6. Andersson, L., Porath, J., Isolation of phosphoproteins by immobilized metal (Fe31) affinity chromatography. Anal. Biochem. 1986, 154, 250-254.
7. Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E. et al., Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. USA 2004, 101, 12130-12135.
8. Rush, J., Moritz, A., Lee, K. A., Guo, A. et al., Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol. 2004.
9. Blagoev, B., Ong, S. E., Kratchmarova, I., Mann, M., Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol. 2004, 22, 1139-1145.
10. Hinsby, A. M., Olsen, J. V., Bennett, K. L., Mann, M., Signaling initiated by overexpression of the fibroblast growth factor receptor-1 investigated by mass spectrometry. Mol. Cell. Proteomics 2003, 2, 29-36.
11. Ibarrola, N., Molina, H., Iwahori, A., Pandey, A., A novel proteomic approach for specific identification of tyrosine kinase substrates using 13C-labeled tyrosine. J. Biol. Chem. 2004.
12. Hinsby, A. M., Olsen, J. V., Mann, M., Tyrosine phosphoproteomics of fibroblast growth factor signaling: A role for insulin receptor substrate-4. J. Biol. Chem. 2004, 279, 46438-46447.
13. Matsuoka, S., Ballif, B. A., Smogorzewska, A., McDonald, E. R., III et al., ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007, 316, 1160-1166.
14. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J. et al., Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 2002, 20, 301-305.
15. Ficarro, S. B., Salomon, A. R., Brill, L. M., Mason, D. E. et al., Automated immobilized metal affinity chromatography/ nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites. Rapid Commun. Mass Spectrom. 2005, 19, 57-71.
16. Larsen, M. R., Thingholm, T. E., Jensen, O. N., Roepstorff, P., Jorgensen, T. J., Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell. Proteomics 2005, 4, 873-886.
17. Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P. et al., Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 2005, 4, 310-327.
18. Ballif, B. A., Villen, J., Beausoleil, S. A., Schwartz, D., Gygi, S. P., Phosphoproteomic analysis of the developing mouse brain. Mol. Cell. Proteomics 2004, 3, 1093-1101.
19. Motoyama, A., Xu, T., Ruse, C. I., Wohlschlegel, J. A., Yates, J. R., III, Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides. Anal. Chem. 2007, 79, 3623-3634.
20. Oda, Y., Nagasu, T., Chait, B. T., Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 2001, 19, 379-382.
21. Tao, W. A., Wollscheid, B., O'Brien, R., Eng, J. K. et al., Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat. Methods 2005, 2, 591-598.
22. Bodenmiller, B., Mueller, L. N., Pedrioli, P. G., Pflieger, D. et al., An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: Application to Drosophila melanogaster Kc167 cells. Mol. Biosyst. 2007, 3, 275-286.
23. Schmelzle, K., Kane, S., Gridley, S., Lienhard, G. E., White, F. M., Temporal dynamics of tyrosine phosphorylation in insulin signaling. Diabetes 2006, 55, 2171-2179.
24. Kim, J. E., White, F. M., Quantitative analysis of phosphotyrosine signaling networks triggered by CD3 and CD28 costimulation in Jurkat cells. J. Immunol. 2006, 176, 2833-2843.
25. Wolf-Yadlin, A., Kumar, N., Zhang, Y., Hautaniemi, S. et al., Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol. Syst. Biol. 2006, 2, 54.
26. Zhang, Y., Wolf-Yadlin, A., Ross, P. L., Pappin, D. J. et al., Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell. Proteomics 2005, 4, 1240-1250.
27. Choe, L., D'Ascenzo, M., Relkin, N. R., Pappin, D. et al., 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics 2007, 7, 3651-3660.
28. Ong, S. E., Mann, M., A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Protoc. 2006, 1, 2650-2660.
29. 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.
30. Kerner, M. J., Naylor, D. J., Ishihama, Y., Maier, T. et al., Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 2005, 122, 209-220.
31. Nirmalan, N., Sims, P. F., Hyde, J. E., Quantitative proteomics of the human malaria parasite Plasmodium falciparum and its application to studies of development and inhibition. Mol. Microbiol. 2004, 52, 1187-1199.
32. Gruhler, A., Schulze, W. X., Matthiesen, R., Mann, M., Jensen, O. N., Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Mol. Cell. Proteomics 2005, 4, 1697-1709.
33. Krijgsveld, J., Ketting, R. F., Mahmoudi, T., Johansen, J. et al., Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat. Biotechnol. 2003, 21, 927-931.
34. Wu, C. C., MacCoss, M. J., Howell, K. E., Matthews, D. E., Yates, J. R., III, Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal. Chem. 2004, 76, 4951-4959.
35. Barnidge, D. R., Hall, G. D., Stocker, J. L., Muddiman, D. C., Evaluation of a cleavable stable isotope labeled synthetic peptide for absolute protein quantification using LC-MS/MS. J. Proteome Res. 2004, 3, 658-661.
36. Beynon, R. J., Doherty, M. K., Pratt, J. M., Gaskell, S. J., Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2005, 2, 587-589.
37. Pratt, J. M., Simpson, D. M., Doherty, M. K., Rivers, J. et al., Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat. Protoc. 2006, 1, 1029-1043.
38. Mirzaei, H., McBee, J., Watts, J., Aebersold, R., Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol. Cell. Proteomics 2007, 7, 813-823.
39. Foster, L. J., de Hoog, C. L., Zhang, Y., Zhang, Y. et al., A mammalian organelle map by protein correlation profiling. Cell 2006, 125, 187-199.
40. 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.
41. Mallick, P., Schirle, M., Chen, S. S., Flory, M. R. et al., Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 2007, 25, 125-131.
42. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
43. Zubarev, R. A., Horn, D. M., Fridriksson, E. K., Kelleher, N. L. et al., Electron capture dissociation for structural characterization of multiply charged protein cations. Anal. Chem. 2000, 72, 563-573.
44. Syka, J. E., Coon, J. J., Schroeder, M. J., Shabanowitz, J., Hunt, D. F., Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 2004, 101, 9528-9533.
45. Wolf-Yadlin, A., Hautaniemi, S., Lauffenburger, D. A., White, F. M., Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl. Acad. Sci. USA 2007, 104, 5860-5865.
46. Olsen, J. V., Macek, B., Lange, O., Makarov, A. et al., Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods 2007, 4, 709-712.
47. Yarden, Y., Sliwkowski, M. X., Untangling the ErbB signalling network. Nat. Rev. Mol. Cell Biol. 2001, 2, 127-137.
48. Rikova, K., Guo, A., Zeng, Q., Possemato, A. et al., Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 2007, 131, 1190-1203.
49. Soda, M., Choi, Y. L., Enomoto, M., Takada, S. et al., Identification of the transforming EML4-ALK fusion gene in nonsmall-cell lung cancer. Nature 2007, 448, 561-566.
50. Olsen, J. V., Blagoev, B., Gnad, F., Macek, B. et al., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648.
51. Yaffe, M. B., White, F. M., Signaling netwErks get the global treatment. Genome Biol. 2007, 8, 202.
52. Friedman, A., Perrimon, N., A functional RNAi screen for regulators of receptor tyrosine kinase and ERK signalling. Nature 2006, 444, 230-234.
53. Elias, J. E., Haas, W., Faherty, B. K., Gygi, S. P., Comparative evaluation of mass spectrometry platforms used in largescale proteomics investigations. Nat. Methods 2005, 2, 667-675.
54. Kumar, N., Wolf-Yadlin, A., White, F. M., Lauffenburger, D. A., Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput. Biol. 2007, 3, e4.
55. Kratchmarova, I., Blagoev, B., Haack-Sorensen, M., Kassem, M., Mann, M., Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science 2005, 308, 1472-1477.
56. Huang, P. H., Mukasa, A., Bonavia, R., Flynn, R. A. et al., Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc. Natl. Acad. Sci. USA 2007, 104, 12867-12872.
57. Stommel, J. M., Kimmelman, A. C., Ying, H., Nabioullin, R. et al., Coactivation of receptor tyrosine kinases affects the response of tumor cells to targeted therapies. Science 2007, 318, 287-290.
58. Bantscheff, M., Eberhard, D., Abraham, Y., Bastuck, S. et al., Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 2007, 25, 1035-1044.
59. Zhou, H., Watts, J. D., Aebersold, R., A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 2001, 19, 375-378.
60. Chi, A., Huttenhower, C., Geer, L. Y., Coon, J. J. et al., Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci. USA 2007, 104, 2193-2198.