Skip to main content

What are the Common Mass Spectrometry-Based Analyses Used in Biology?

  • Chapter
  • First Online:
Mass Spectrometry: Developmental Approaches to Answer Biological Questions

Part of the book series: SpringerBriefs in Bioengineering ((BRIEFSBIOENG))

  • 1351 Accesses

Abstract

Mass spectrometry is used in many field of research, such as biology, chemistry, geology, etc. The focus of this chapter is the common methods, requiring mass spectrometry, in biology related researches. Proteomics for example is a field of research focusing on proteins for which mass spectrometry plays a pivotal role. However, proteins are not the unique target, lipids and small compounds such as metabolites are also studied using mass spectrometry. As we are now in the era of ‘omics’ the field of research studying lipids is called lipidomics and the analysis of metabolites is known as metabolomics. Through the example of the main methods used in proteomics analysis, this chapter summarizes the advantages of mass spectrometry in biology research. The analyses of small biomolecules, lipids and nucleotides are also presented.

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

Access this chapter

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. Hua L, Low TY, Sze SK. Microwave-assisted specific chemical digestion for rapid protein identification. Proteomics. 2006;6(2):586–91.

    Google Scholar 

  2. Anderson L, Anderson NG. High resolution two-dimensional electrophoresis of human plasma proteins. Proc Natl Acad Sci U S A. 1977;74(12):5421–5.

    Google Scholar 

  3. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics. 2002;1(11):845–67.

    Google Scholar 

  4. Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, Aebersold R. The quantitative proteome of a human cell line. Mol Syst Biol. 2011;8(7):549.

    Google Scholar 

  5. Pottiez G, Deracinois B, Duban-Deweer S, Cecchelli R, Fenart L, Karamanos Y, Flahaut C. A large-scale electrophoresis- and chromatography-based determination of gene expression profiles in bovine brain capillary endothelial cells after the re-induction of blood-brain barrier properties. Proteome Sci. 2010;15(8):57.

    Google Scholar 

  6. O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975;250(10):4007–21.

    Google Scholar 

  7. O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975;250(10):4007–21.

    Google Scholar 

  8. Roepstorff P, Fohlman J Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom. 1984;11(11):601.

    Google Scholar 

  9. Johnson RS, Martin SA, Biemann K, Stults JT, Watson JT. Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine. Anal Chem. 1987;59(21):2621–5.

    Google Scholar 

  10. Zubarev RA, Kelleher NL, McLafferty FW. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J Am Chem Soc. 1998;120(13):3265–66.

    Google Scholar 

  11. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A. 2004;101(26):9528–33.

    Google Scholar 

  12. Cook SL, Collin OL, Jackson GP. Metastable atom-activated dissociation mass spectrometry: leucine/isoleucine differentiation and ring cleavage of proline residues. J Mass Spectrom. 2009;44(8):1211–23.

    Google Scholar 

  13. Karsch-Mizrachi I, Ouellette BF. The GenBank sequence database. Methods Biochem Anal. 2001;43:45–63.

    Google Scholar 

  14. Chelius D, Bondarenko PV. Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res. 2002;1(4):317–23.

    Google Scholar 

  15. Bondarenko PV, Chelius D, Shaler TA. Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem. 2002;74(18):4741–9.

    Google Scholar 

  16. Wang W, Zhou H, Lin H, Roy S, Shaler TA, Hill LR, Norton S, Kumar P, Anderle M, Becker CH. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem. 2003;75(18):4818–26.

    Google Scholar 

  17. Liu H, Sadygov RG, Yates JR. 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem. 2004;76(14):4193–201.

    Google Scholar 

  18. Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem. 2007;389(4):1017–31.

    Google Scholar 

  19. Ryu S, Gallis B, Goo YA, Shaffer SA, Radulovic D, Goodlett DR. Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method. Cancer Inform. 2008;6:243–55.

    Google Scholar 

  20. Klein PD, Haumann JR, Eisler WJ. Instrument design considerations and clinical applications of stable isotope analysis. Clin Chem. 1971;17(8):735–9.

    Google Scholar 

  21. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999;17(10):994–9.

    Google Scholar 

  22. Unwin RD, Pierce A, Watson RB, Sternberg DW, Whetton AD. Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells. Mol Cell Proteomics. 2005;4(7):924–35.

    Google Scholar 

  23. Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser DF, Burkhard PR, Sanchez JC. Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal Chem. 2008;80(8):2921–31.

    Google Scholar 

  24. Schmidt A, Kellermann J, Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics. 2005;5(1):4–15.

    Google Scholar 

  25. Capelo JL, Carreira RJ, Fernandes L, Lodeiro C, Santos HM, Simal-Gandara J. Latest developments in sample treatment for 18O-isotopic labeling for proteomics mass spectrometry-based approaches: a critical review. Talanta. 2010;80(4):1476–8.

    Google Scholar 

  26. Bonzon-Kulichenko E, Pérez-Hernández D, Núñez E, Martínez-Acedo P, Navarro P, Trevisan-Herraz M, Ramos Mdel C, Sierra S, Martínez-Martínez S, Ruiz-Meana M, Miró-Casas E, García-Dorado D, Redondo JM, Burgos JS, Vázquez J. A robust method for quantitative high-throughput analysis of proteomes by 18O labeling. Mol Cell Proteomics. 2011;10(1):M110.003335.

    Google Scholar 

  27. Kirkpatrick DS, Gerber SA, Gygi SP. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods. 2005;35(3):265–73.

    Google Scholar 

  28. lipidlibrary.aocs.org

    Google Scholar 

  29. Yang SF, Chang CW, Wei RJ, Shiue YL, Wang SN, Yeh YT. Involvement of DNA damage response pathways in hepatocellular carcinoma. Biomed Res Int. 2014;2014:153867. (Epub 2014 Apr 28).

    Google Scholar 

  30. Li LF, Chan RL, Lu L, Shen J, Zhang L, Wu WK, Wang L, Hu T, Li MX, Cho CH. Cigarette smoking and gastrointestinal diseases: The causal relationship and underlying molecular mechanisms (Review). Int J Mol Med. 2014;34(2):372–80.

    Google Scholar 

  31. Porru S, Pavanello S, Carta A, Arici C, Simeone C, Izzotti A, Mastrangelo G. Complex relationships between occupation, environment, DNA adducts, genetic polymorphisms and bladder cancer in a case-control study using a structural equation modeling. PLoS ONE. 2014;9(4):e94566.

    Google Scholar 

  32. Zhang F, Bartels MJ, Pottenger LH, Gollapudi BB, Schisler MR. Quantitation of lower levels of the DNA adduct of thymidylyl(3'-5')thymidine methyl phosphotriester by liquid chromatography/negative atmospheric pressure chemical ionization tandem mass spectrometry. Rapid Commun Mass Spectrom. 2007;21(6):1043–8.

    Google Scholar 

  33. Tretyakova N, Villalta PW, Kotapati S. Mass spectrometry of structurally modified DNA. Chem Rev. 2013;113(4):2395–436.

    Google Scholar 

  34. Cerny RL, Tomer KB, Gross ML, Grotjahn L. Fast atom bombardment combined with tandem mass spectrometry for determining structures of small oligonucleotides. Anal Biochem. 1987;165(1):175–82.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gwenael Pottiez .

Rights and permissions

Reprints and permissions

Copyright information

© 2015 The Author

About this chapter

Cite this chapter

Pottiez, G. (2015). What are the Common Mass Spectrometry-Based Analyses Used in Biology?. In: Mass Spectrometry: Developmental Approaches to Answer Biological Questions. SpringerBriefs in Bioengineering. Springer, Cham. https://doi.org/10.1007/978-3-319-13087-3_2

Download citation

Publish with us

Policies and ethics