Selected Reaction Monitoring Applied to Quantitative Proteomics

  • Reiko Kiyonami
  • Bruno Domon
Part of the Methods in Molecular Biology book series (MIMB, volume 658)


Proteomics is gradually shifting from pure qualitative studies (protein identification) to large-scale quantitative experiments, prompted by the growing need to analyze consistently and precisely a large set of proteins in biological samples. The selected reaction monitoring (SRM) technique is increasingly applied to quantitative proteomics because of its selectivity (two levels of mass selection), its sensitivity (non-scanning mode), and its wide dynamic range. This account describes the different steps in the design and the experimental setup of SRM experiments.

Key words

Selective reaction monitoring (SRM) quantitative proteomics triple quadrupole isotopically labeled internal standards 



Dr. Andreas Huhmer and David Fischer are gratefully acknowledged for helpful discussion.


  1. 1.
    Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., and Gygi, S. P. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 100, 6940–6945.PubMedCrossRefGoogle Scholar
  2. 2.
    Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., and Aebersold, R. (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795–806.PubMedCrossRefGoogle Scholar
  3. 3.
    Anderson, N. L., Polanski, M., Pieper, R., Gatlin, T., Tirumalai, R. S., Conrads, T. P., Veenstra, T. D., Adkins, J. N., Pounds, J. G., Fagan, R., and Lobley, A. (2004) The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol. Cell. Proteomics 3, 311–326.PubMedCrossRefGoogle Scholar
  4. 4.
    Stahl-Zeng, J., Lange, V., Ossola, R., Eckhardt, K., Krek, W., Aebersold, R., and Domon, B. (2007) High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 6 1809–1817.PubMedCrossRefGoogle Scholar
  5. 5.
    Prakash, A., Kiyonami, R., Shoen, A., Nguyen, H., Peterman, S., Huhmer, A., Lopez, M., and Domon, B. (2009) Integrated workflow to design methods and analyze data in large-to-extremely-large scale SRM experiments. Proc. ASMS 2009 Poster, TH695.Google Scholar
  6. 6.
    Wojcik, J., and Schächter, V. (2000) Proteomic databases and software on the web. Oxford J. Brief Bioinform. 1, 250–259.Google Scholar
  7. 7.
    Krokhin, O. V., Craig, R., Spicer, V., Ens, W., Standing, K. G., Beavis, R. C., and Wilkins, J. A. (2004) An improved model for prediction of retention times of tryptic peptides in ion-pair reverse-phase HPLC: its application to protein peptide mapping by off-line HPLC–MALDI MS. Mol. Cell. Proteomics 3, 908–319.Google Scholar
  8. 8.
    Chalkley, R.J., Baker, P. R., Medzihradszky, K. F., Lynn, A. J., and Burlingame, A. L. (2008) In-depth analysis of tandem mass spectrometry data from disparate instrument types. Mol. Cell. Proteomics 7, 2386–2398.PubMedCrossRefGoogle Scholar
  9. 9.
    Picotti, P., Lam, H., Campbell, D., Deutsch, E. W., Mirzaei, H., Ranish, J., Domon, B., and Aebersold, R. (2008) A database of mass spectrometric assays for the yeast proteome. Nat. Methods 5, 913–914.PubMedCrossRefGoogle Scholar
  10. 10.
    Pratt, J. M., Simpson, D. M., Doherty, M. K., Rivers, J., Gaskell, S. J., and Beynon, R. J. (2006) Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat. Protoc. 1, 1029–1043.PubMedCrossRefGoogle Scholar
  11. 11.
    Prakash, A., Tomazela, D. M., Frewen, B., Maclean, B., Merrihew, G., Peterman, S., Maccoss, M. J. (2008) Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J. Proteome Res. 8, 2733–2739.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Reiko Kiyonami
    • 1
  • Bruno Domon
    • 2
  1. 1.ThermoFisher ScientificSan JoseUSA
  2. 2.IMSB – ETH ZurichZurichSwitzerland

Personalised recommendations