4. Mass Spectrometry and Protein Identification

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

Published Online: 10 JAN 2013

DOI: 10.1002/9781118494042.ch4

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) Mass Spectrometry and Protein Identification, in Computational and Statistical Methods for Protein Quantification by Mass Spectrometry, John Wiley & Sons Ltd, Oxford, UK. doi: 10.1002/9781118494042.ch4

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:

  • false discovery rate (FDR);
  • mass spectrometry (MS);
  • peptide identification;
  • protein identification

Summary

This chapter provides a brief overview of the principles of using mass spectrometry (MS) for protein identification and characterization. It focuses on isotopes of carbon, and assumes that all the other elements (hydrogen, nitrogen, oxygen, phosphorus, and sulfur) are always represented by their lightest isotope. Quantification of proteins is based on the intensities of the peaks in the spectra, thus high quality intensity calculation is required, and this calculation should be based on the raw data. The chapter gives a brief introduction to the task of protein identification. An MS/MS spectrum for a peptide is created by splitting the peptide into smaller fragments, and producing a spectrum of the fragments being ionized. The chapter discusses step by step procedure for estimating false discovery rate (FDR).

Controlled Vocabulary Terms

Computational statistics; Inferential statistics