Skip to main content
SpringerLink
Log in

Introduction to Quantitative Proteomics

  • Chapter
  • First Online:
Application of Selected Reaction Monitoring to Highly Multiplexed Targeted Quantitative Proteomics

Part of the book series: SpringerBriefs in Systems Biology ((BRIEFSBIOSYS))

  • 881 Accesses

Abstract

The use of mass spectrometry for quantitative analysis began with the very first published experiment in 1913. Therefore, current applications, including quantitative proteomics, are based on an extensive foundation of fundamental and applied investigations. This history also applies to selected reaction monitoring. The ability of tandem mass spectrometry to enhance the specificity of an analysis was apparent in the 1970s and the technique has a strong history of use for many classes of small molecules. As a result, the application of selected reaction monitoring to targeted quantitative proteomics can be seen as a straight-forward experiment based on sound principles, excellent equipment, and a distinguished history.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Thomson JJ (1913) Rays of positive electricity. Proc R Soc 89:1–20

    Article  CAS  Google Scholar 

  2. Kinter M, Sherman NE (2000) Protein sequencing and identification using tandem mass spectrometry. Wiley, New York

    Book  Google Scholar 

  3. Liu H, Sadygov RG, Yates JR 3rd (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76:4193–4201

    Article  PubMed  CAS  Google Scholar 

  4. Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, Shukla AK, Smith RD, Waters KM, McDermott JE, Webb-Robertson BJ (2013) A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics 13:493–503

    Article  PubMed  CAS  Google Scholar 

  5. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999

    Article  PubMed  CAS  Google Scholar 

  6. Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C (2001) Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 73:2836–2842

    Article  PubMed  CAS  Google Scholar 

  7. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154–1169

    Article  PubMed  CAS  Google Scholar 

  8. Wühr M, Haas W, McAlister GC, Peshkin L, Rad R, Kirschner MW, Gygi SP (2012) Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster. Anal Chem 84:9214–9221

    PubMed  Google Scholar 

  9. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376–386

    Article  PubMed  CAS  Google Scholar 

  10. Geiger T, Velic A, Macek B, Lundberg E, Kampf C, Nagaraj N, Uhlen M, Cox J, Mann M. (2013) Initial quantitative proteomic map of twenty-eight mouse tissues using the SILAC mouse. Mol Cell Proteomics 12:1709–1722

    Google Scholar 

  11. Washburn MP, Wolters D, Yates JR 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242–247

    Article  PubMed  CAS  Google Scholar 

  12. Michalski A, Cox J, Mann M (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res 10:1785–1793

    Article  PubMed  CAS  Google Scholar 

  13. Editors (2013) Method of the Year 2012. Nat Methods 10:1

    Google Scholar 

  14. Picotti P, Bodenmiller B, Aebersold R (2013) Proteomics meets the scientific method. Nat Methods 10:24–27

    Article  PubMed  CAS  Google Scholar 

  15. Gillette MA, Carr SA (2013) Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat Methods 10:28–34

    Article  PubMed  CAS  Google Scholar 

  16. Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA (2009) Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 27:633–641

    Article  PubMed  CAS  Google Scholar 

  17. Beynon JH, Cooks RG, Amy JW, Baitinger WE, Ridley TY (1973) Design and performance of a mass-analyzed ion kinetic energy (MIKE) spectrometer. Anal Chem 45:1023A–1031A

    Article  Google Scholar 

  18. McLafferty FW, Bente PF 3rd, Kornfeld R, Tsai S-C, Howe I (1973) Collision activation spectra of organic ions. J Am Chem Soc 95:2120–2129

    Article  CAS  Google Scholar 

  19. Yost RA, Enke CG (1979) Triple quadrupole mass spectrometry for direct mixture analysis and structure elucidation. Anal Chem 51:1251–1264

    Article  PubMed  CAS  Google Scholar 

  20. Kruger TL, Litton JF, Kondrat RW, Cooks RG (1976) Mixture analysis by mass-analyzed ion kinetic energy spectrometry. Anal Chem 48:2113–2119

    Article  CAS  Google Scholar 

  21. Kondrat RW, Cooks RG, McLaughlin JL (1978) Alkaloids in whole plant material: direct analysis by kinetic energy spectrometry. Science 199:978–980

    Article  PubMed  CAS  Google Scholar 

  22. Brotherton HO, Yost RA (1983) Determination of drugs in blood serum by mass spectrometry/mass spectrometry. Anal Chem 55:549–553

    Article  PubMed  CAS  Google Scholar 

  23. Johnson JV, Yost RA, Faull KF (1984) Tandem mass spectrometry for the trace determination of tryptolines in crude brain extracts. Anal Chem 56:1655–1661

    Article  PubMed  CAS  Google Scholar 

  24. Kalkum M, Lyon GJ, Chait BT (2003) Detection of secreted peptides by using hypothesis-driven multistage mass spectrometry. Proc Natl Acad Sci USA 100:2795–2800

    Article  PubMed  CAS  Google Scholar 

  25. Yi Z, Luo M, Carroll CA, Weintraub ST, Mandarino LJ (2005) Identification of phosphorylation sites in insulin receptor substrate-1 by hypothesis-driven high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. Anal Chem 77:5693–5699

    Article  PubMed  CAS  Google Scholar 

  26. Roof RW, Haskell MD, Dukes BD, Sherman N, Kinter M, Parsons SJ (1998) Phosphotyrosine (p-Tyr)-dependent and -independent mechanisms of p190 RhoGAP-p120 RasGAP interaction: Tyr 1105 of p190, a substrate for c-Src, is the sole p-Tyr mediator of complex formation. Mol Cell Biol 18:7052–7063

    PubMed  CAS  Google Scholar 

  27. Ruse CI, Willard B, Jin JP, Haas T, Kinter M, Bond M (2002) Quantitative dynamics of site-specific protein phosphorylation determined using liquid chromatography electrospray ionization mass spectrometry. Anal Chem 74:1658–1664

    Article  PubMed  CAS  Google Scholar 

  28. Willard BB, Ruse CI, Keightley JA, Bond M, Kinter M (2003) Site-specific quantitation of protein nitration using liquid chromatography/tandem mass spectrometry. Anal Chem 75:2370–2376

    Article  PubMed  CAS  Google Scholar 

  29. Arnott D, Kishiyama A, Luis EA, Ludlum SG, Marsters JC Jr, Stults JT (2002) Selective detection of membrane proteins without antibodies: a mass spectrometric version of the Western blot. Mol Cell Proteomics 1:148–156

    Article  PubMed  CAS  Google Scholar 

  30. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100:6940–6945

    Article  PubMed  CAS  Google Scholar 

  31. Barnidge DR, Goodmanson MK, Klee GG, Muddiman DC (2004) Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry. J Proteome Res 3:644–652

    Article  PubMed  CAS  Google Scholar 

  32. Anderson L, Hunter CL (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 5:573–588

    PubMed  CAS  Google Scholar 

  33. Whiteaker JR, Zhang H, Zhao L, Wang P, Kelly-Spratt KS, Ivey RG, Piening BD, Feng LC, Kasarda E, Gurley KE, Eng JK, Chodosh LA, Kemp CJ, McIntosh MW, Paulovich AG (2007) Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res 6:3962–3975

    Article  PubMed  CAS  Google Scholar 

  34. Kinter M (2004) Toward a broader inclusion of liquid chromatography-mass spectrometry in the clinical laboratory. Clin Chem 50:1500–1502

    Article  PubMed  CAS  Google Scholar 

  35. MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26:966–968

    Article  PubMed  CAS  Google Scholar 

  36. Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R (2006) The PeptideAtlas project. Nucleic Acids Res 34:D655–D658

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Oklahoma Medical Research Foundation, Oklahoma City, OK, USA

    Michael Kinter & Caroline S. Kinter

Authors
  1. Michael Kinter
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Caroline S. Kinter
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this chapter

Cite this chapter

Kinter, M., Kinter, C.S. (2013). Introduction to Quantitative Proteomics. In: Application of Selected Reaction Monitoring to Highly Multiplexed Targeted Quantitative Proteomics. SpringerBriefs in Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8666-4_1

Download citation

Publish with us

Policies and ethics

Search

Navigation