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The pros and cons of peptide-centric proteomics

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Recommendations on how best to exploit the strengths of peptide-centric proteomics and avoid its pitfalls.

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Figure 1: General approach used by peptide-centric MS technologies for the identification of proteins in complex mixtures.
Figure 2: Representation of sequence coverage for a protein identified using a peptide-centric approach.

References

  1. Nedelkov, D. et al. Proc. Natl. Acad. Sci. USA 102, 10852–10857 (2005).

    Article  CAS  Google Scholar 

  2. Krishna, R.G. & Wold, F. Adv. Enzymol. 67, 265–298 (1993).

    CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. Picotti, P., Aebersold, R. & Domon, B. Mol. Cell. Proteomics 6, 1589–1598 (2007).

    Article  CAS  Google Scholar 

  5. Carr, S. et al. Mol. Cell. Proteomics 3, 531–533 (2004).

    Article  CAS  Google Scholar 

  6. Andersen, J.S. & Mann, M. EMBO Rep. 7, 874–879 (2006).

    Article  CAS  Google Scholar 

  7. Wilkins, M.R. et al. Proteomics 6, 4–8 (2006).

    Article  CAS  Google Scholar 

  8. Shen, Y. et al. Anal. Chem. 80, 1871–1882 (2008).

    Article  CAS  Google Scholar 

  9. Keller, A., Nesvizhskii, A.I., Kolker, E. & Aebersold, R. Anal. Chem. 74, 5383–5392 (2002).

    Article  CAS  Google Scholar 

  10. Elias, J.E. & Gygi, S.P. Nat. Methods 4, 207–214 (2007).

    Article  CAS  Google Scholar 

  11. Nesvizhskii, A.I. & Aebersold, R. Mol. Cell. Proteomics 4, 1419–1440 (2005).

    Article  CAS  Google Scholar 

  12. Whaley, B. & Caprioli, R.M. Biol. Mass Spectrom. 20, 210–214 (1991).

    Article  CAS  Google Scholar 

  13. Chamrad, D. & Meyer, H.E. Nat. Methods 2, 647–648 (2005).

    Article  CAS  Google Scholar 

  14. Elias, J.E., Haas, W., Faherty, B.K. & Gygi, S.P. Nat. Methods 2, 667–675 (2005).

    Article  CAS  Google Scholar 

  15. Schmidt, A., Claassen, M. & Aebersold, R. Curr. Opin. Chem. Biol. 13, 510–517 (2009).

    Article  CAS  Google Scholar 

  16. Hackett, M. Proteomics 8, 4618–4623 (2008).

    Article  CAS  Google Scholar 

  17. Duncan, M.W., Yergey, A.L. & Patterson, S.D. Proteomics 9, 1124–1127 (2009).

    Article  CAS  Google Scholar 

  18. Schulze, W.X. & Usadel, B. Annu. Rev. Plant Biol. 61, 491–516 (2010).

    Article  CAS  Google Scholar 

  19. Liu, H., Sadygov, R.G. & Yates, J.R., III. Anal. Chem. 76, 4193–4201 (2004).

    Article  CAS  Google Scholar 

  20. Braisted, J.C. et al. BMC Bioinformatics 9, 529 (2008).

    Article  Google Scholar 

  21. Chelius, D. & Bondarenko, P.V. J. Proteome Res. 1, 317–323 (2002).

    Article  CAS  Google Scholar 

  22. Bondarenko, P.V., Chelius, D. & Shaler, T.A. Anal. Chem. 74, 4741–4749 (2002).

    Article  CAS  Google Scholar 

  23. Settlage, R.E. et al. PRG-2009: Relative Protein Quantification in a Clinical Matrix (ABRF, Proteomics Research Group, 2009) <http://www.abrf.org/ResearchGroups/Proteomics/EPosters/PRG2009_poster.pdf>.

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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Acknowledgements

We thank R. Nelson, A. Yergey and I. Krull for their insightful and constructive comments on early drafts of this manuscript.

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Authors and Affiliations

  1. Mark W. Duncan is in the Division of Endocrinology, Metabolism and Diabetes School of Medicine, University of Colorado Denver, Aurora, Colorado, USA and the Obesity Research Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,

    Mark W Duncan

  2. Ruedi Aebersold is at ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland.,

    Ruedi Aebersold

  3. Richard M. Caprioli is in the Department of Biochemistry and at the Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.,

    Richard M Caprioli

Authors
  1. Mark W Duncan
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  2. Ruedi Aebersold
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  3. Richard M Caprioli
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Correspondence to Richard M Caprioli.

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The authors declare no competing financial interests.

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Duncan, M., Aebersold, R. & Caprioli, R. The pros and cons of peptide-centric proteomics. Nat Biotechnol 28, 659–664 (2010). https://doi.org/10.1038/nbt0710-659

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