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The biological impact of mass-spectrometry-based proteomics

Nature volume 450, pages 991–1000 (2007)Cite this article

Abstract

In the past decade, there have been remarkable advances in proteomic technologies. Mass spectrometry has emerged as the preferred method for in-depth characterization of the protein components of biological systems. Using mass spectrometry, key insights into the composition, regulation and function of molecular complexes and pathways have been gained. From these studies, it is clear that mass-spectrometry-based proteomics is now a powerful 'hypothesis-generating engine' that, when combined with complementary molecular, cellular and pharmacological techniques, provides a framework for translating large data sets into an understanding of complex biological processes.

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Figure 1: Discovery of a BAD-containing protein complex that localizes to mitochondria and integrates apoptotic and glycolytic processes.
Figure 2: Discovery of Tfb5 as the tenth subunit of TFIIH, which is involved in transcriptional and DNA-repair processes.
Figure 3: Discovery of chaperone complexes that regulate CFTR folding and endoplasmic-reticulum-mediated export.
Figure 4: Identification of male-gametocyte-specific and female-gametocyte-specific proteins in Plasmodium berghei.
Figure 5: Discovery of an ether-lipid signalling pathway that supports cancer pathogenesis.
Figure 6: Identification of candidate ATM and/or ATR substrates involved in the DNA-damage response.
Figure 7: Discovery of DAF-2-regulated protein pathways that modulate longevity in Caenorhabditis elegans.

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References

  1. Whisstock, J. C. & Lesk, A. M. Prediction of protein function from protein sequence and structure. Q. Rev. Biophys. 36, 307–340 (2003).

    Article  CAS  Google Scholar 

  2. Galperin, M. Y. & Koonin, E. V. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res. 32, 5452–5463 (2004).

    Article  CAS  Google Scholar 

  3. Zhu, H., Bilgin, M. & Snyder, M. Proteomics. Annu. Rev. Biochem. 72, 783–812 (2003).

    Article  CAS  Google Scholar 

  4. de Hoog, C. L. & Mann, M. Proteomics. Annu. Rev. Genomics Hum. Genet. 5, 267–293 (2004).

    Article  CAS  Google Scholar 

  5. MacBeath, G. Protein microarrays and proteomics. Nature Genet. 32 (suppl.), 526–532 (2002).

    Article  CAS  Google Scholar 

  6. Hall, D. A., Ptacek, J. & Snyder, M. Protein microarray technology. Mech. Ageing Dev. 128, 161–167 (2007).

    Article  CAS  Google Scholar 

  7. Causier, B. Studying the interactome with the yeast two-hybrid system and mass spectrometry. Mass Spectrom. Rev. 23, 350–367 (2004).

    Article  ADS  Google Scholar 

  8. Stevens, R. C., Yokoyama, S. & Wilson, I. A. Global efforts in structural genomics. Science 294, 89–92 (2001).

    Article  CAS  ADS  Google Scholar 

  9. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).

    Article  CAS  ADS  Google Scholar 

  10. Yates, J. R. Mass spectral analysis in proteomics. Annu. Rev. Biophys. Biomol. Struct. 33, 297–316 (2004).

    Article  CAS  Google Scholar 

  11. Domon, B. & Aebersold, R. Mass spectrometry and protein analysis. Science 312, 212–217 (2006).

    Article  CAS  ADS  Google Scholar 

  12. Andersen, J. S. & Mann, M. Organellar proteomics: turning inventories into insights. EMBO Rep. 7, 874–879 (2006).

    Article  CAS  Google Scholar 

  13. Cusick, M. E., Klitgord, N., Vidal, M. & Hill, D. E. Interactome: gateway into systems biology. Hum. Mol. Genet. 14, R171–R181 (2005).

    Article  CAS  Google Scholar 

  14. Michnick, S. W. Proteomics in living cells. Drug Discov. Today 9, 262–267 (2004).

    Article  CAS  Google Scholar 

  15. Neubauer, G. et al. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nature Genet. 20, 46–50 (1998).

    Article  CAS  Google Scholar 

  16. Wang, Y. et al. BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. Genes Dev. 14, 927–939 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Rout, M. P. et al. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148, 635–651 (2000).

    Article  CAS  Google Scholar 

  18. Bouwmeester, T. et al. A physical and functional map of the human TNF-α/NF-κB signal transduction pathway. Nature Cell Biol. 6, 97–105 (2004).

    Article  CAS  Google Scholar 

  19. Das, R. et al. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol. Cell 26, 867–881 (2007).

    Article  CAS  Google Scholar 

  20. Danial, N. N. et al. BAD and glucokinase reside in a mitochondrial complex that integrates glycolysis and apoptosis. Nature 424, 952–956 (2003).

    Article  CAS  ADS  Google Scholar 

  21. Harada, H. et al. Phosphorylation and inactivation of BAD by mitochondria-anchored protein kinase A. Mol. Cell 3, 413–422 (1999).

    Article  CAS  Google Scholar 

  22. Gatenby, R. A. & Gillies, R. J. Why do cancers have high aerobic glycolysis? Nature Rev. Cancer 4, 891–899 (2004).

    Article  CAS  Google Scholar 

  23. Wang, X. The expanding role of mitochondria in apoptosis. Genes Dev. 15, 2922–2933 (2001).

    CAS  PubMed  Google Scholar 

  24. Coulombe, B., Jeronimo, C., Langelier, M. F., Cojocaru, M. & Bergeron, D. Interaction networks of the molecular machines that decode, replicate, and maintain the integrity of the human genome. Mol. Cell. Proteomics 3, 851–856 (2004).

    Article  CAS  Google Scholar 

  25. Ranish, J. A. et al. Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nature Genet. 36, 707–713 (2004).

    Article  CAS  Google Scholar 

  26. Gygi, S. P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17, 994–999 (1999).

    Article  CAS  Google Scholar 

  27. Cenkci, B., Petersen, J. L. & Small, G. D. REX1, a novel gene required for DNA repair. J. Biol. Chem. 278, 22574–22577 (2003).

    Article  CAS  Google Scholar 

  28. Giglia-Mari, G. et al. A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nature Genet. 36, 714–719 (2004).

    Article  CAS  Google Scholar 

  29. Vermeulen, W. et al. Sublimiting concentration of TFIIH transcription/DNA repair factor causes TTD-A trichothiodystrophy disorder. Nature Genet. 26, 307–313 (2000).

    Article  CAS  Google Scholar 

  30. Krogan, N. J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae . Nature 440, 637–643 (2006).

    Article  CAS  ADS  Google Scholar 

  31. Krebs, M. P., Noorwez, S. M., Malhotra, R. & Kaushal, S. Quality control of integral membrane proteins. Trends Biochem. Sci. 29, 648–655 (2004).

    Article  CAS  Google Scholar 

  32. Kelly, J. W. & Balch, W. E. The integration of cell and chemical biology in protein folding. Nature Chem. Biol. 2, 224–227 (2006).

    Article  CAS  Google Scholar 

  33. Riordan, J. R. Assembly of functional CFTR chloride channels. Annu. Rev. Physiol. 67, 701–718 (2005).

    Article  CAS  Google Scholar 

  34. Qu, B. H., Strickland, E. H. & Thomas, P. J. Localization and suppression of a kinetic defect in cystic fibrosis transmembrane conductance regulator folding. J. Biol. Chem. 272, 15739–15744 (1997).

    Article  CAS  Google Scholar 

  35. Loo, M. A. et al. Perturbation of Hsp90 interaction with nascent CFTR prevents its maturation and accelerates its degradation by the proteasome. EMBO J. 17, 6879–6887 (1998).

    Article  CAS  Google Scholar 

  36. Meacham, G. C., Patterson, C., Zhang, W., Younger, J. M. & Cyr, D. M. The Hsc70 co-chaperone CHIP targets immature CFTR for proteasomal degradation. Nature Cell Biol. 3, 100–105 (2001).

    Article  CAS  Google Scholar 

  37. Wang, X. et al. Hsp90 cochaperone Aha1 downregulation rescues misfolding of CFTR in cystic fibrosis. Cell 127, 803–815 (2006).

    Article  CAS  Google Scholar 

  38. Washburn, M. P., Wolters, D. & Yates, J. R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol. 19, 242–247 (2001).

    Article  CAS  Google Scholar 

  39. Hanash, S. Disease proteomics. Nature 422, 226–232 (2003).

    Article  CAS  ADS  Google Scholar 

  40. Kumar, N. et al. Molecular complexity of sexual development and gene regulation in Plasmodium falciparum . Int. J. Parasitol. 34, 1451–1458 (2004).

    Article  CAS  Google Scholar 

  41. Khan, S. M. et al. Proteome analysis of separated male and female gametocytes reveals novel sex-specific Plasmodium biology. Cell 121, 675–687 (2005).

    Article  CAS  Google Scholar 

  42. Ward, P., Equinet, L., Packer, J. & Doerig, C. Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics 5, 79 (2004).

    Article  Google Scholar 

  43. Jessani, N. & Cravatt, B. F. The development and application of methods for activity-based protein profiling. Curr. Opin. Chem. Biol. 8, 54–59 (2004).

    Article  CAS  Google Scholar 

  44. Jessani, N., Liu, Y., Humphrey, M. & Cravatt, B. F. Enzyme activity profiles of the secreted and membrane proteome that depict cancer invasiveness. Proc. Natl Acad. Sci. USA 99, 10335–10340 (2002).

    Article  CAS  ADS  Google Scholar 

  45. Liu, Y., Patricelli, M. P. & Cravatt, B. F. Activity-based protein profiling: the serine hydrolases. Proc. Natl Acad. Sci. USA 96, 14694–14699 (1999).

    Article  CAS  ADS  Google Scholar 

  46. Patricelli, M. P., Giang, D. K., Stamp, L. M. & Burbaum, J. J. Direct visualization of serine hydrolase activities in complex proteome using fluorescent active site-directed probes. Proteomics 1, 1067–1071 (2001).

    Article  CAS  Google Scholar 

  47. Jessani, N. et al. A streamlined platform for high-content functional proteomics of primary human specimens. Nature Methods 2, 691–697 (2005).

    Article  CAS  Google Scholar 

  48. Leung, D., Hardouin, C., Boger, D. L. & Cravatt, B. F. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nature Biotechnol. 21, 687–691 (2003).

    Article  CAS  Google Scholar 

  49. Saghatelian, A. et al. Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry 43, 14332–14339 (2004).

    Article  CAS  Google Scholar 

  50. Chiang, K. P., Niessen, S., Saghatelian, A. & Cravatt, B. F. An enzyme that regulates ether lipid signaling pathways in cancer annotated by multidimensional profiling. Chem. Biol. 13, 1041–1050 (2006).

    Article  CAS  Google Scholar 

  51. Manning, G., Whyte, D. B., Martinez, R., Hunter, T. & Sudarsanam, S. The protein kinase complement of the human genome. Science 298, 1912–1934 (2002).

    Article  CAS  ADS  Google Scholar 

  52. Matsuoka, S. et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316, 1160–1166 (2007).

    Article  CAS  ADS  Google Scholar 

  53. Shiloh, Y. The ATM-mediated DNA-damage response: taking shape. Trends Biochem. Sci. 31, 402–410 (2006).

    Article  CAS  Google Scholar 

  54. Oda, Y., Huang, K., Cross, F. R., Cowburn, D. & Chait, B. T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl Acad. Sci. USA 96, 6591–6596 (1999).

    Article  CAS  ADS  Google Scholar 

  55. Mann, M. Functional and quantitative proteomics using SILAC. Nature Rev. Mol. Cell Biol. 7, 952–958 (2006).

    Article  CAS  Google Scholar 

  56. Wang, B. et al. Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response. Science 316, 1194–1198 (2007).

    Article  CAS  ADS  Google Scholar 

  57. Smogorzewska, A. et al. Identification of the FANCI protein, a monoubiquitinated FANCD2 paralog required for DNA repair. Cell 129, 289–301 (2007).

    Article  CAS  Google Scholar 

  58. Olsen, J. V. et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635–648 (2006).

    Article  CAS  Google Scholar 

  59. Rush, J. et al. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nature Biotechnol. 23, 94–101 (2005).

    Article  CAS  Google Scholar 

  60. Jin, M. et al. Quantitative analysis of protein phosphorylation in mouse brain by hypothesis-driven multistage mass spectrometry. Anal. Chem. 77, 7845–7851 (2005).

    Article  CAS  Google Scholar 

  61. Huang, P. H. et al. Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc. Natl Acad. Sci. USA 104, 12867–12872 (2007).

    Article  CAS  ADS  Google Scholar 

  62. Kim, S. C. et al. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol. Cell 23, 607–618 (2006).

    Article  CAS  Google Scholar 

  63. Garcia, B. A., Pesavento, J. J., Mizzen, C. A. & Kelleher, N. L. Pervasive combinatorial modification of histone H3 in human cells. Nature Methods 4, 487–489 (2007).

    Article  CAS  Google Scholar 

  64. Ong, S. E., Mittler, G. & Mann, M. Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nature Methods 1, 119–126 (2004).

    Article  CAS  Google Scholar 

  65. Khidekel, N. et al. Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics. Nature Chem. Biol. 3, 339–348 (2007).

    Article  CAS  Google Scholar 

  66. Peng, J. et al. A proteomics approach to understanding protein ubiquitination. Nature Biotechnol. 21, 921–926 (2003).

    Article  CAS  Google Scholar 

  67. Mukhopadhyay, A. & Tissenbaum, H. A. Reproduction and longevity: secrets revealed by C. elegans . Trends Cell Biol. 17, 65–71 (2007).

    Article  CAS  Google Scholar 

  68. Kenyon, C., Chang, J., Gensch, E., Rudner, A. & Tabtiang, R. A C. elegans mutant that lives twice as long as wild type. Nature 366, 461–464 (1993).

    Article  CAS  ADS  Google Scholar 

  69. Dong, M. Q. et al. Quantitative mass spectrometry identifies new insulin targets in C. elegans . Science 317, 660–663 (2007).

    Article  CAS  ADS  Google Scholar 

  70. Venable, J. D., Dong, M. Q., Wohlschlegel, J., Dillin, A. & Yates, J. R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nature Methods 1, 39–45 (2004).

    Article  CAS  Google Scholar 

  71. Liu, H., Sadygov, R. G. & Yates, J. R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193–4201 (2004).

    Article  CAS  Google Scholar 

  72. Wu, C. C., MacCoss, M. J., Howell, K. E., Matthews, D. E. & Yates, J. R. Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal. Chem. 76, 4951–4959 (2004).

    Article  CAS  Google Scholar 

  73. Berns, K. et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428, 431–437 (2004).

    Article  CAS  ADS  Google Scholar 

  74. Perrimon, N. & Mathey-Pervot, B. Applications of high-throughput RNA interference screens to problems in cell and developmental biology. Genetics 175, 7–16 (2007).

    Article  CAS  Google Scholar 

  75. Zabrouskov, V., Senko, M. W., Du, Y., Leduc, R. D. & Kelleher, N. L. New and automated MS n approaches for top-down identification of modified proteins. J. Am. Soc. Mass Spectrom. 16, 2027–2038 (2005).

    Article  CAS  Google Scholar 

  76. Conrads, T. P., Anderson, G. A., Veenstra, T. D., Pasa-Tolic, L. & Smith, R. D. Utility of accurate mass tags for proteome-wide protein identification. Anal. Chem. 72, 3349–3354 (2000).

    Article  CAS  Google Scholar 

  77. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W. & Gygi, S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl Acad. Sci. USA 100, 6940–6945 (2003).

    Article  CAS  ADS  Google Scholar 

  78. MacCoss, M. J. et al. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl Acad. Sci. USA 99, 7900–7905 (2002).

    Article  CAS  ADS  Google Scholar 

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Acknowledgements

We gratefully acknowledge the support of the National Institutes of Health.

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Authors and Affiliations

  1. Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA

    Benjamin F. Cravatt, Gabriel M. Simon & John R. Yates III

  2. The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA

    Benjamin F. Cravatt & Gabriel M. Simon

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Correspondence should be addressed to B.F.C. (cravatt@scripps.edu) or J.R.Y. (jyates@scripps.edu).

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Cravatt, B., Simon, G. & Yates III, J. The biological impact of mass-spectrometry-based proteomics. Nature 450, 991–1000 (2007). https://doi.org/10.1038/nature06525

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