Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Commentary
  • Published:

Proteomics meets the scientific method

By delivering precise, reproducible quantification of proteins of interest in biological samples, targeted proteomics approaches are allowing researchers to apply the scientific method using mass spectrometry.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The scientific method and proteomic analyses.

References

  1. Sumner, J.B. J. Biol. Chem. 69, 435–441 (1926).

    CAS  Google Scholar 

  2. Lander, E.S. et al. Nature 409, 860–921 (2001).

    Article  CAS  Google Scholar 

  3. Aebersold, R. & Mann, M. Nature 422, 198–207 (2003).

    Article  CAS  Google Scholar 

  4. Bodenmiller, B. et al. Nat. Methods 4, 231–237 (2007).

    Article  CAS  Google Scholar 

  5. Gerber, S.A. et al. Proc. Natl. Acad. Sci. USA 100, 6940–6945 (2003).

    Article  CAS  Google Scholar 

  6. Ong, S.E. et al. Mol. Cell. Proteomics 1, 376–386 (2002).

    Article  CAS  Google Scholar 

  7. Gygi, S.P. et al. Nat. Biotechnol. 17, 994–999 (1999).

    Article  CAS  Google Scholar 

  8. Lemeer, S. & Heck, A.J. Curr. Opin. Chem. Biol. 13, 414–420 (2009).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. Edwards, A.M. et al. Nature 470, 163–165 (2011).

    Article  CAS  Google Scholar 

  11. Anderson, L. & Hunter, C.L. Mol. Cell. Proteomics 5, 573–588 (2006).

    Article  CAS  Google Scholar 

  12. Picotti, P. & Aebersold, R. Nat. Methods 9, 555–566 (2012).

    Article  CAS  Google Scholar 

  13. Bisson, N. et al. Nat. Biotechnol. 29, 653–658 (2011).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  15. Wolf-Yadlin, A. et al. Proc. Natl. Acad. Sci. USA 104, 5860–5865 (2007).

    Article  CAS  Google Scholar 

  16. Wang, Q. et al. Proc. Natl. Acad. Sci. USA 108, 2444–2449 (2011).

    Article  CAS  Google Scholar 

  17. Costenoble, R. et al. Mol. Syst. Biol. 7, 464 (2011).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  19. Picotti, P. et al. Cell 138, 795–806 (2009).

    Article  CAS  Google Scholar 

  20. Ebhardt, H.A. et al. Proteomics 12, 1185–1193 (2012).

    Article  CAS  Google Scholar 

  21. Wang, Q. et al. Proc. Natl. Acad. Sci. USA 108, 2444–2449 (2011).

    Article  CAS  Google Scholar 

  22. Picotti, P. et al. Nature (in the press).

  23. Zulak, K.G. et al. Plant J. 60, 1015–1030 (2009).

    Article  CAS  Google Scholar 

  24. Liu, T. et al. J. Proteomics 75, 4747–4757 (2012).

    Article  CAS  Google Scholar 

  25. Chen, Y. et al. J. Proteome Res. 9, 4215–4227 (2010).

    Article  CAS  Google Scholar 

  26. Altvater, M. et al. Mol. Syst. Biol. (in the press).

  27. Whiteaker, J.R. et al. Nat. Biotechnol. 29, 625–634 (2011).

    Article  CAS  Google Scholar 

  28. Keshishian, H. et al. Mol. Cell. Proteomics 8, 2339–2349 (2009).

    Article  CAS  Google Scholar 

  29. Gillet, L.C., et al. Mol. Cell. Proteomics 11, O111.016717 (2012).

    Article  Google Scholar 

  30. Gallien, S. et al. Mol. Cell. Proteomics published online, doi:10.1074/mcp.O112.019802 (7 September 2012).

  31. Peterson, A.C. et al. Mol. Cell. Proteomics 11, 1475–1488 (2012).

    Article  Google Scholar 

  32. Cravatt, B.F., Wright, A.T. & Kozarich, J.W. Annu. Rev. Biochem. 77, 383–414 (2008).

    Article  CAS  Google Scholar 

  33. Cornett, D.S. et al. Nat. Methods 4, 828–833 (2007).

    Article  CAS  Google Scholar 

  34. Bendall, S.C. et al. Science 332, 687–696 (2011).

    Article  CAS  Google Scholar 

  35. Bodenmiller, B. et al. Nat. Biotechnol. 30, 858–867 (2012).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ruedi Aebersold.

Ethics declarations

Competing interests

P.P. and R.A. hold shares of the company BioGnosys, which operates in the field covered by the article. The research group of R.A. is supported by the company AB/Sciex and receives access to prototype instrumentation.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Picotti, P., Bodenmiller, B. & Aebersold, R. Proteomics meets the scientific method. Nat Methods 10, 24–27 (2013). https://doi.org/10.1038/nmeth.2291

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.2291

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing