5. Protein Quantification by Mass Spectrometry

  1. Ingvar Eidhammer,
  2. Harald Barsnes,
  3. Geir Egil Eide and
  4. Lennart Martens

Published Online: 10 JAN 2013

DOI: 10.1002/9781118494042.ch5

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry

How to Cite

Eidhammer, I., Barsnes, H., Eide, G. E. and Martens, L. (2013) Protein Quantification by Mass Spectrometry, in Computational and Statistical Methods for Protein Quantification by Mass Spectrometry, John Wiley & Sons Ltd, Oxford, UK. doi: 10.1002/9781118494042.ch5

Publication History

  1. Published Online: 10 JAN 2013
  2. Published Print: 4 JAN 2013

ISBN Information

Print ISBN: 9781119964001

Online ISBN: 9781118494042

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Keywords:

  • ion chromatograms;
  • mass spectrometry;
  • peptide variants;
  • protein abundances;
  • protein quantification;
  • replicates

Summary

Protein quantification consists of performing experiments to determine proteome and/or protein profiles. This chapter provides numerous methods for classifying protein quantification by mass spectrometry, and gives brief explanations of the different approaches. The purpose of replicates is to eliminate random variations in order to achieve precise measurements of the subject under consideration, for example, the effect of different treatments for a disease. A quantification experiment is performed by several mass spectrometry analyses, called runs. Mass spectrometry quantification experiments can roughly be divided into two main tasks: Identification and quantification. The protein abundances are calculated from the abundances of the peptide variants. In many quantification methods peak intensities from successive spectra are combined, and the combined intensities are shown as chromatograms, often called ion chromatograms. The chapter discusses the most serious issues related to which peptides should be used in calculating the protein abundances.

Controlled Vocabulary Terms

Computational statistics; Inferential statistics