Protein Quantitation Using Mass Spectrometry

  • Guoan Zhang
  • Beatrix M. Ueberheide
  • Sofia Waldemarson
  • Sunnie Myung
  • Kelly Molloy
  • Jan Eriksson
  • Brian T. Chait
  • Thomas A. Neubert
  • David FenyöEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 673)


Mass spectrometry is a method of choice for quantifying low-abundance proteins and peptides in many biological studies. Here, we describe a range of computational aspects of protein and peptide quantitation, including methods for finding and integrating mass spectrometric peptide peaks, and detecting interference to obtain a robust measure of the amount of proteins present in samples.

Key words

Proteomics Quantitation Proteins Peptides Mass spectrometry 



This work was supported by funding provided by the National Institutes of Health Grants RR00862, RR022220, NS050276, and CA126485, the Carl Trygger foundation, and the Swedish research council.


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Guoan Zhang
    • 1
  • Beatrix M. Ueberheide
    • 2
  • Sofia Waldemarson
    • 1
  • Sunnie Myung
    • 2
  • Kelly Molloy
    • 2
  • Jan Eriksson
    • 3
  • Brian T. Chait
    • 2
  • Thomas A. Neubert
    • 1
  • David Fenyö
    • 2
    Email author
  1. 1.Kimmel Center for Biology and Medicine at the Skirball Institute and Department of PharmacologyNew York University School of MedicineNew YorkUSA
  2. 2.The Rockefeller UniversityNew YorkUSA
  3. 3.Department of ChemistrySwedish University of Agricultural SciencesUppsalaSweden

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