Mass Spectrometry of Proteins and Peptides

  • Kenneth G. Standing
Part of the Springer Protocols Handbooks book series (SPH)

1. Introduction

In the last few years, mass spectrometry (MS) has emerged as a major tool for the identification and characterization of peptides and proteins. It is now possible to measure proteins of masses > 100 kDa to an accuracy of a few Da, and to measure the masses of peptides with an accuracy of a few mDa. As a result, the information yielded by an MS measurement is highly specific. In addition, MS has extremely high sensitivity, often in the femtomole (10−15 mole) range, so it is a method that is suitable for the analysis of trace amounts of sample.

Mass spectrometry relies on the properties of charged particles moving under the influence of electric and magnetic fields, so the species studied must be ions (charge ze) rather than molecules. Most MS experiments are performed on positive ions, which can be formed either by the removal of one or more electrons from each molecule, or by the addition of one or more cations, usually protons. Consequently, the first step in any mass...


Quadrupole Mass Filter Magnetic Sector Mass Spectrometer Pulse Laser Fire Linear Quadrupole Mass Filter Symmetric Electrostatic Field 
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  1. 1.
    McClosky JA (ed) (1990) Methods in enzymology, vol. 193: mass spectrometry. Academic Press, New York, N.Y. pp. 1–960Google Scholar
  2. 2.
    Cotter RJ (1997) Time-of-flight mass spectrometry: instrumentation and applications in biological research. American Chemical SocietyGoogle Scholar
  3. 3.
    Tang X, Beavis R, Ens W, Lafortune F, Schueler B, Standing KG (1988) A Secondary Ion Time-of-Flight Mass Spectrometer with an Ion Mirror. Int J Mass Spectrom Ion Processes 85:43–67CrossRefGoogle Scholar
  4. 4.
    March RE, Todd JFJ (2005) Quadrupole ion trap mass spectrometry, 2nd edn., John Wiley and Sons, Hoboken, NJCrossRefGoogle Scholar
  5. 5.
    Marshall AG, Hendrickson CL, Jackson GS (1998) Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom Rev 17:1–35PubMedCrossRefGoogle Scholar
  6. 6.
    Borchers CH, Marquez VE, Schroeder GK, Short SA, Snider MJ, Speir JP, Wolfenden R (2004) Fourier transform ion cyclotron resonance MS reveals the presence of a water molecule in an enzyme transition-state analogue complex. Proc Natl Acad Sci U S A. 101:15,341–15,3415CrossRefGoogle Scholar
  7. 7.
    Makarov A (2000) Electrostatic axially harmonic orbital trapping: a high- performance technique of mass analysis. Anal Chem 72:1156–1162PubMedCrossRefGoogle Scholar
  8. 8.
    Scigelova M, Makarov A (2006) Orbitrap mass analyzer – overview and applications in proteomics. Proteomics 6 Suppl:2 16–21PubMedCrossRefGoogle Scholar
  9. 9.
    Kinter M, Sherman, NE (2000) Protein sequencing and identification using tandem mass spectrometry. Wiley-Interscience, New York, NYCrossRefGoogle Scholar
  10. 10.
    Standing KG (2003) Peptide and protein de novo sequencing by mass spectrom-etry. Curr Opin Struct Biol 13:595–601PubMedCrossRefGoogle Scholar
  11. 11.
    Wysocki VH, Resing KA, Zhang Q, Cheng G (2005) Mass spectrometry of pep-tides and proteins. Methods 35:211–222PubMedCrossRefGoogle Scholar
  12. 12.
    Yost RA, Boyd RK (1990) Tandem mass spectrometry: quadrupole and hybrid instruments. In: (McClosky JA (ed) Methods in enzymology, vol. 193: mass spectrometry. Academic Press, New York, NY, pp 154–200Google Scholar
  13. 13.
    Chernushevich IV, Loboda AV, Thomson BA (2001) An introduction to quadrupole-time-of-flight mass spectrometry. J Mass Spectrom 36:849–865PubMedCrossRefGoogle Scholar
  14. 14.
    Ens W, Standing KG (2005) Hybrid quadrupole time-of-flight mass spectrometers for analysis of biomolecules. In: Burlingame AL (ed) Methods in enzymology, vol. 402: biological mass spectrometry. pp 49–78Google Scholar
  15. 15.
    Chernushevich IV, Ens W, Standing KG. (1999). Orthogonal Injection TOFMS for Analyzing Biomolecules. Anal Chem 71:452A–461ACrossRefGoogle Scholar
  16. 16.
    Vestal ML, Campbell JM (2005) Tandem time-of-flight mass spectrometry. In: Burlingame AL (ed) Methods in enzymology, vol. 402: biological mass spectrometry. pp. 79–108Google Scholar
  17. 17.
    Jebanathirajah JA, Pittman JL, Thomson BA, Budnik BA, Kaur P, Rape M, Kirschner M, Costello CE, O'Connor PB (2005). Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins. J Am Soc Mass Spectrom 16:1985–1999PubMedCrossRefGoogle Scholar
  18. 18.
    Ferguson PL, Smith RD (2003) Proteome analysis by mass spectrometry. Annu Rev Biophys Biomol Struct 32:399–424PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Kenneth G. Standing
    • 1
  1. 1.Department of Physics and AstronomyUniversity of ManitobaWinnipeg, ManitobaCanada

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