Current trends in quantitative proteomics

J Mass Spectrom. 2009 Dec;44(12):1637-60. doi: 10.1002/jms.1692.


It was inevitable that as soon as mass spectrometrists were able to tell biologists which proteins were in their samples, the next question would be how much of these proteins were present. This has turned out to be a much more challenging question. In this review, we describe the multiple ways that mass spectrometry has attempted to address this issue, both for relative quantitation and for absolute quantitation of proteins. There is no single method that will work for every problem or for every sample. What we present here is a variety of techniques, with guidelines that we hope will assist the researcher in selecting the most appropriate technique for the particular biological problem that needs to be addressed. We need to emphasize that this is a very active area of proteomics research-new quantitative methods are continuously being introduced and some 'pitfalls' of older methods are just being discovered. However, even though there is no perfect technique--and a better technique may be developed tomorrow--valuable information on biomarkers and pathways can be obtained using these currently available methods.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Fluorescent Dyes
  • Humans
  • Isotope Labeling
  • Mass Spectrometry / methods*
  • Nitrogen Isotopes
  • Oxygen Isotopes
  • Peptide Fragments / analysis
  • Peptide Fragments / metabolism
  • Peptide Hydrolases / metabolism
  • Proteomics / methods*
  • Proteomics / trends*
  • Sensitivity and Specificity
  • Software
  • Spectrometry, Mass, Electrospray Ionization
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Tandem Mass Spectrometry


  • Fluorescent Dyes
  • Nitrogen Isotopes
  • Oxygen Isotopes
  • Peptide Fragments
  • Peptide Hydrolases