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.
References
Aebersold, R. & Mann, M. Nature 422, 198–207 (2003).
Altelaar, A.F., Munoz, J. & Heck, A.J. Nat. Rev. Genet. 14, 35–48 (2013).
Mann, M., Kulak, N.A., Nagaraj, N. & Cox, J. Mol. Cell 49, 583–590 (2013).
Cutillas, P.R. & Timms, J.F. Methods Mol. Biol. 658, 1–357 (2010).
Bantscheff, M., Lemeer, S., Savitski, M.M. & Kuster, B. Anal. Bioanal. Chem. 404, 939–965 (2012).
Leon, I.R., Schwammle, V., Jensen, O.N. & Sprenger, R.R. Mol. Cell. Proteomics 12, 2992–3005 (2013).
Sandra, K. et al. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 866, 48–63 (2008).
Nagaraj, N. et al. Mol. Cell. Proteomics 11, M111013722 (2012).
Scigelova, M. & Makarov, A. Proteomics 6 (suppl. 2), 16–21 (2006).
Ens, W. & Standing, K.G. Methods Enzymol. 402, 49–78 (2005).
Lange, V., Picotti, P., Domon, B. & Aebersold, R. Mol. Syst. Biol. 4, 222 (2008).
Peterson, A.C., Russell, J.D., Bailey, D.J., Westphall, M.S. & Coon, J.J. Mol. Cell. Proteomics 11, 1475–1488 (2012).
Olsen, J.V. et al. Nat. Methods 4, 709–712 (2007).
Mikesh, L.M. et al. Biochim. Biophys. Acta 1764, 1811–1822 (2006).
Luber, C.A. et al. Immunity 32, 279–289 (2010).
Hettinger, J. et al. Nat. Immunol. 14, 821–830 (2013).
Meissner, F., Scheltema, R.A., Mollenkopf, H.J. & Mann, M. Science 340, 475–478 (2013).
Gupta, N. et al. Nat. Immunol. 7, 625–633 (2006).
Trost, M. et al. Immunity 30, 143–154 (2009).
Gingras, A.C., Gstaiger, M., Raught, B. & Aebersold, R. Nat. Rev. Mol. Cell Biol. 8, 645–654 (2007).
Pichlmair, A. et al. Nature 487, 486–490 (2012).
Li, S., Wang, L., Berman, M., Kong, Y.Y. & Dorf, M.E. Immunity 35, 426–440 (2011).
Plasman, K., Van Damme, P. & Gevaert, K. Curr. Opin. Chem. Biol. 17, 66–72 (2013).
Navarro, M.N., Goebel, J., Feijoo-Carnero, C., Morrice, N. & Cantrell, D.A. Nat. Immunol. 12, 352–361 (2011).
Chevrier, N. et al. Cell 147, 853–867 (2011).
Hoppes, R., Ekkebus, R., Schumacher, T.N. & Ovaa, H. J. Proteomics 73, 1945–1953 (2010).
Altelaar, A.F. & Heck, A.J. Curr. Opin. Chem. Biol. 16, 206–213 (2012).
Ong, S.E. et al. Mol. Cell. Proteomics 1, 376–386 (2002).
Howden, A.J. et al. Nat. Methods 10, 343–346 (2013).
Geiger, T. et al. Nat. Protoc. 6, 147–157 (2011).
Trudgian, D.C. et al. Proteomics 11, 2790–2797 (2011).
Cox, J. & Mann, M. Nat. Biotechnol. 26, 1367–1372 (2008).
Sadygov, R.G., Cociorva, D. & Yates, J.R. III . Nat. Methods 1, 195–202 (2004).
Elias, J.E. & Gygi, S.P. Nat. Methods 4, 207–214 (2007).
Bradshaw, R.A., Burlingame, A.L., Carr, S. & Aebersold, R. Mol. Cell. Proteomics 5, 787–788 (2006).
Olsen, J.V. & Mann, M. Sci. Signal. 4, pe7 (2011).
Rebsamen, M., Kandasamy, R.K. & Superti-Furga, G. Trends Immunol. 12, 610–619 (2013).
Diercks, A. & Aderem, A. Curr. Top. Microbiol. Immunol. 363, 1–19 (2013).
Amit, I., Regev, A. & Hacohen, N. Nat. Rev. Immunol. 11, 873–880 (2011).
Heng, T.S.P. et al. Nat. Immunol. 9, 1091–1094 (2008).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Rights and permissions
About this article
Cite this article
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
Published:
Issue Date:
DOI: https://doi.org/10.1038/ni.2781
- Springer Nature America, Inc.
This article is cited by
-
A genetic engineering strategy for editing near-infrared-II fluorophores
Nature Communications (2022)
-
Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies
Cellular & Molecular Immunology (2019)
-
Proteomic study revealed cellular assembly and lipid metabolism dysregulation in sepsis secondary to community-acquired pneumonia
Scientific Reports (2017)
-
Regulation of intestinal homeostasis by the ulcerative colitis-associated gene RNF186
Mucosal Immunology (2017)
-
Unbiased Quantitative Proteomics Reveals a Crucial Role of the Allergen Context for the Activation of Human Dendritic Cells
Scientific Reports (2017)