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Mass Spectrometry of Proteins (Proteomics)

Proteins, Peptides and Amino Acids

  1. Hiroyuki Matsumoto1,
  2. Sadamu Kurono1,
  3. Masaomi Matsumoto2,
  4. Naoka Komori1

Published Online: 15 SEP 2006

DOI: 10.1002/3527600906.mcb.200400079

Reviews in Cell Biology and Molecular Medicine

Reviews in Cell Biology and Molecular Medicine

How to Cite

Matsumoto, H., Kurono, S., Matsumoto, M. and Komori, N. 2006. Mass Spectrometry of Proteins (Proteomics). Reviews in Cell Biology and Molecular Medicine. .

Author Information

  1. 1

    The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA

  2. 2

    Oklahoma Department of Agriculture, Oklahoma City, OK, USA

Publication History

  1. Published Online: 15 SEP 2006


The completion of genome projects represents a pinnacle of human enterprise in the biosciences. The orchestration of technologies in mass spectrometry, genome science, and computer sciences has created a new branch of molecular bioscience called proteomics. A proteomics approach to the study of protein expression and posttranslational modification does not require foreknowledge of the identity of target proteins. A proteomic investigation begins with the discovery of unidentified proteins of interest under well-defined physiological conditions. The approach involves (1) protein display by 2-D gel electrophoresis or other separation technique; (2) determination of protein entities of interest; (3) peptide mass fingerprinting (PMF); and (4) genome/proteome database search. The methodology of the proteomics approach is characterized neither by deduction nor by induction in the traditional sense, but is a clear example of what C. S. Peirce described as abductive inference a century ago. The investigation of molecular and cellular events is often intractable to deductive and inductive methods due to its extreme complexity and nonlinearity. Proteomics is a powerful tool to study complex biological systems because of its characteristics: (1) no a priori knowledge of the protein's identity is required to initiate a project; and (2) a holistic approach is possible for investigation. It is expected that proteomics will substantially contribute to the future development of molecular medicine.


  • Abductive Inference or Abduction;
  • Collision Induced Dissociation or MS/MS;
  • Electrospray Ionization;
  • Endopeptidase;
  • Genome;
  • Mass Spectrometry/Mass Spectrometer;
  • Matrix-Assisted Laser Desorption/Ionization;
  • Peptide Mass Fingerprinting;
  • Post Source Decay;
  • Posttranslational Modification;
  • Proteome;
  • Proteomics;
  • Two-dimensional Gel Electrophoresis;
  • U