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Mass spectrometry in high-throughput proteomics: ready for the big time

Mass spectrometry has evolved and matured to a level where it is able to assess the complexity of the human proteome. We discuss some of the expected challenges ahead and promising strategies for success.

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References

  1. Clamp, M. et al. Proc. Natl. Acad. Sci. USA 104, 19428–19433 (2007).

    Article  CAS  Google Scholar 

  2. Anonymous. Nature 452, 913–914 (2008).

  3. Petricoin, E.F. et al. Lancet 359, 572–577 (2002).

    Article  CAS  Google Scholar 

  4. Bell, A.W. et al. Nat. Methods 6, 423–430 (2009).

    Article  CAS  Google Scholar 

  5. Mann, M. Nat. Methods 6, 717–719 (2009).

    Article  CAS  Google Scholar 

  6. Domon, B. & Aebersold, R. Nat. Biotechnol. 28, 710–721 (2010).

    Article  CAS  Google Scholar 

  7. Addona, T.A. et al. Nat. Biotechnol. 27, 633–641 (2009).

    Article  CAS  Google Scholar 

  8. Westman-Brinkmalm, A. et al. Front. Biosci. 14, 1793–1806 (2009).

    Article  CAS  Google Scholar 

  9. Nettikadan, S. et al. Mol. Cell. Proteomics 5, 895–901 (2006).

    Article  CAS  Google Scholar 

  10. Tabb, D.L. et al. J. Proteome Res. 9, 761–776 (2010).

    Article  CAS  Google Scholar 

  11. Ingolia, N.T., Ghaemmaghami, S., Newman, J.R.S. & Weissman, J.S. Science 324, 218–223 (2009).

    Article  CAS  Google Scholar 

  12. Denny, P. et al. J. Proteome Res. 7, 1994–2006 (2008).

    Article  CAS  Google Scholar 

  13. Brunner, E. et al. Nat. Biotechnol. 25, 576–583 (2007).

    Article  CAS  Google Scholar 

  14. Durr, E. et al. Nat. Biotechnol. 22, 985–992 (2004).

    Article  CAS  Google Scholar 

  15. de Godoy, L.M. et al. Nature 455, 1251–1254 (2008).

    Article  CAS  Google Scholar 

  16. Tabb, D.L. J. Proteome Res. 7, 45–46 (2008).

    Article  CAS  Google Scholar 

  17. Brusniak, M.Y. et al. BMC Bioinformatics 9, 542 (2008).

    Article  Google Scholar 

  18. Reiter, L. et al. Mol. Cell. Proteomics 8, 2405–2417 (2009).

    Article  CAS  Google Scholar 

  19. Takamori, S. et al. Cell 127, 831–846 (2006).

    Article  CAS  Google Scholar 

  20. Silva, J.C., Gorenstein, M.V., Li, G.-Z., Vissers, J.P.C. & Geromanos, S.J. Mol. Cell. Proteomics 5, 144–156 (2006).

    Article  CAS  Google Scholar 

  21. Blondeau, F. et al. Proc. Natl. Acad. Sci. USA 101, 3833–3838 (2004).

    Article  CAS  Google Scholar 

  22. Gilchrist, A. et al. Cell 127, 1265–1281 (2006).

    Article  CAS  Google Scholar 

  23. Krüger, M. et al. Cell 134, 353–364 (2008).

    Article  Google Scholar 

  24. McClatchy, D.B., Dong, M.-Q., Wu, C.C., Venable, J.D. & Yates, J.R. III J. Proteome Res. 6, 2005–2010 (2007).

    Article  CAS  Google Scholar 

  25. Kuster, B., Schirle, M., Mallick, P. & Aebersold, R. Nat. Rev. Mol. Cell Biol. 6, 577–583 (2005).

    Article  CAS  Google Scholar 

  26. Picotti, P. et al. Nat. Methods 5, 913–914 (2008).

    Article  CAS  Google Scholar 

  27. Malmstrom, J. et al. Nature 460, 762–765 (2009).

    Article  Google Scholar 

  28. Picotti, P. et al. Nat. Methods 7, 43–46 (2010).

    Article  CAS  Google Scholar 

  29. Portelius, E. et al. J. Proteome Res. 7, 2114–2120 (2008).

    Article  CAS  Google Scholar 

  30. Whiteaker, J.R., Zhao, L., Anderson, L. & Paulovich, A.P. Mol. Cell. Proteomics 9, 184–196 (2010).

    Article  CAS  Google Scholar 

  31. Collins, F.S., Green, E.D., Guttmacher, A.E. & Guyer, M.S. Nature 422, 835–847 (2003).

    Article  CAS  Google Scholar 

  32. International Human Genome Sequencing Consortium. Nature 431, 931–945 (2004).

  33. Gregory, S.G. et al. Nature 441, 315–321 (2006).

    Article  CAS  Google Scholar 

  34. Hill, J.A., Smith, B.E., Papoulias, P.G. & Andrews, P.C. J. Proteome Res. 9, 2809–2811 (2010).

    Article  CAS  Google Scholar 

  35. Desiere, F. et al. Nucleic Acids Res. 34, D655–D658 (2006).

    Article  CAS  Google Scholar 

  36. Ji, L. et al. Nucleic Acids Res. 38, D731–D735 (2010).

    Article  CAS  Google Scholar 

  37. Jones, P. et al. Nucleic Acids Res. 34, D659–D663 (2006).

    Article  CAS  Google Scholar 

  38. Faca, V.M. et al. PLoS Med. 5, e123 (2008).

    Article  Google Scholar 

  39. Sun, A. et al. J. Proteome Res. 9, 50–58 (2010).

    Article  CAS  Google Scholar 

  40. Yoshida, Y., Miyamoto, M., Bo, X., Yaoita, E. & Yamamoto, T. in Proteomics in Nephrology — Towards Clinical Applications (ed. Thongboonkerd, V.) 186–197 (Karger, 2008).

    Google Scholar 

  41. Pontén, F. et al. Mol. Syst. Biol. 5, 337 (2009).

    Article  Google Scholar 

  42. Neumann, B. et al. Nat. Methods 3, 385–390 (2006).

    Article  CAS  Google Scholar 

  43. Starkuviene, V. et al. Methods Mol. Biol. 457, 193–201 (2008).

    Article  CAS  Google Scholar 

  44. Bergeron, J.J., Au, C.E., Desjardins, McPherson, P.S. & Nilsson, T. Trends Cell Biol. 20, 337–345 (2010)

    Article  CAS  Google Scholar 

Download references

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Correspondence to Tommy Nilsson or John J M Bergeron.

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Nilsson, T., Mann, M., Aebersold, R. et al. Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods 7, 681–685 (2010). https://doi.org/10.1038/nmeth0910-681

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