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Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology

Nature Immunology volume 15, pages 112–117 (2014)Cite this article

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Proteomics based on high-resolution mass spectrometry has become a powerful tool for the analysis of protein abundance, modifications and interactions. Here we describe technical aspects of proteomics workflows, instrumentation as well as computational considerations to obtain high-quality proteomics data.

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Figure 1: Cellular and immunological processes that can be studied using proteomics tools.
Figure 2: Shotgun proteomics workflow.
Figure 3: Strategies for quantification of peptides from MS1 spectra.
Figure 4: Computational data analysis.

References

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

    Article  CAS  PubMed  Google Scholar 

  2. Altelaar, A.F., Munoz, J. & Heck, A.J. Nat. Rev. Genet. 14, 35–48 (2013).

    Article  CAS  PubMed  Google Scholar 

  3. Mann, M., Kulak, N.A., Nagaraj, N. & Cox, J. Mol. Cell 49, 583–590 (2013).

    Article  CAS  PubMed  Google Scholar 

  4. Cutillas, P.R. & Timms, J.F. Methods Mol. Biol. 658, 1–357 (2010).

    Google Scholar 

  5. Bantscheff, M., Lemeer, S., Savitski, M.M. & Kuster, B. Anal. Bioanal. Chem. 404, 939–965 (2012).

    Article  CAS  PubMed  Google Scholar 

  6. Leon, I.R., Schwammle, V., Jensen, O.N. & Sprenger, R.R. Mol. Cell. Proteomics 12, 2992–3005 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sandra, K. et al. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 866, 48–63 (2008).

    Article  CAS  PubMed  Google Scholar 

  8. Nagaraj, N. et al. Mol. Cell. Proteomics 11, M111013722 (2012).

    Article  Google Scholar 

  9. Scigelova, M. & Makarov, A. Proteomics 6 (suppl. 2), 16–21 (2006).

    Article  PubMed  Google Scholar 

  10. Ens, W. & Standing, K.G. Methods Enzymol. 402, 49–78 (2005).

    Article  CAS  PubMed  Google Scholar 

  11. Lange, V., Picotti, P., Domon, B. & Aebersold, R. Mol. Syst. Biol. 4, 222 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Peterson, A.C., Russell, J.D., Bailey, D.J., Westphall, M.S. & Coon, J.J. Mol. Cell. Proteomics 11, 1475–1488 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Olsen, J.V. et al. Nat. Methods 4, 709–712 (2007).

    Article  CAS  PubMed  Google Scholar 

  14. Mikesh, L.M. et al. Biochim. Biophys. Acta 1764, 1811–1822 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Luber, C.A. et al. Immunity 32, 279–289 (2010).

    Article  CAS  PubMed  Google Scholar 

  16. Hettinger, J. et al. Nat. Immunol. 14, 821–830 (2013).

    Article  CAS  PubMed  Google Scholar 

  17. Meissner, F., Scheltema, R.A., Mollenkopf, H.J. & Mann, M. Science 340, 475–478 (2013).

    Article  CAS  PubMed  Google Scholar 

  18. Gupta, N. et al. Nat. Immunol. 7, 625–633 (2006).

    Article  CAS  PubMed  Google Scholar 

  19. Trost, M. et al. Immunity 30, 143–154 (2009).

    Article  CAS  PubMed  Google Scholar 

  20. Gingras, A.C., Gstaiger, M., Raught, B. & Aebersold, R. Nat. Rev. Mol. Cell Biol. 8, 645–654 (2007).

    Article  CAS  PubMed  Google Scholar 

  21. Pichlmair, A. et al. Nature 487, 486–490 (2012).

    Article  CAS  PubMed  Google Scholar 

  22. Li, S., Wang, L., Berman, M., Kong, Y.Y. & Dorf, M.E. Immunity 35, 426–440 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Plasman, K., Van Damme, P. & Gevaert, K. Curr. Opin. Chem. Biol. 17, 66–72 (2013).

    Article  CAS  PubMed  Google Scholar 

  24. Navarro, M.N., Goebel, J., Feijoo-Carnero, C., Morrice, N. & Cantrell, D.A. Nat. Immunol. 12, 352–361 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Chevrier, N. et al. Cell 147, 853–867 (2011).

    Article  CAS  PubMed  Google Scholar 

  26. Hoppes, R., Ekkebus, R., Schumacher, T.N. & Ovaa, H. J. Proteomics 73, 1945–1953 (2010).

    Article  CAS  PubMed  Google Scholar 

  27. Altelaar, A.F. & Heck, A.J. Curr. Opin. Chem. Biol. 16, 206–213 (2012).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  29. Howden, A.J. et al. Nat. Methods 10, 343–346 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Geiger, T. et al. Nat. Protoc. 6, 147–157 (2011).

    Article  CAS  PubMed  Google Scholar 

  31. Trudgian, D.C. et al. Proteomics 11, 2790–2797 (2011).

    Article  CAS  PubMed  Google Scholar 

  32. Cox, J. & Mann, M. Nat. Biotechnol. 26, 1367–1372 (2008).

    Article  CAS  PubMed  Google Scholar 

  33. Sadygov, R.G., Cociorva, D. & Yates, J.R. III . Nat. Methods 1, 195–202 (2004).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  35. Bradshaw, R.A., Burlingame, A.L., Carr, S. & Aebersold, R. Mol. Cell. Proteomics 5, 787–788 (2006).

    Article  CAS  PubMed  Google Scholar 

  36. Olsen, J.V. & Mann, M. Sci. Signal. 4, pe7 (2011).

    Article  PubMed  Google Scholar 

  37. Rebsamen, M., Kandasamy, R.K. & Superti-Furga, G. Trends Immunol. 12, 610–619 (2013).

    Article  Google Scholar 

  38. Diercks, A. & Aderem, A. Curr. Top. Microbiol. Immunol. 363, 1–19 (2013).

    CAS  PubMed  Google Scholar 

  39. Amit, I., Regev, A. & Hacohen, N. Nat. Rev. Immunol. 11, 873–880 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Heng, T.S.P. et al. Nat. Immunol. 9, 1091–1094 (2008).

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Felix Meissner and Matthias Mann are in the Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,

    Felix Meissner & Matthias Mann

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  1. Felix Meissner
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  2. Matthias Mann
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Correspondence to Felix Meissner or Matthias Mann.

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Meissner, F., Mann, M. Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology. Nat Immunol 15, 112–117 (2014). https://doi.org/10.1038/ni.2781

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