1. Instrumentation and Developments

  1. Mahmoud Hamdan1 and
  2. Pier Giorgio Righetti2

Published Online: 27 JAN 2005

DOI: 10.1002/0471709158.ch1

Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology

Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology

How to Cite

Hamdan, M. and Righetti, P. G. (2005) Instrumentation and Developments, in Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology, John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/0471709158.ch1

Author Information

  1. 1

    GlaxoSmithKline Research Centre in Verona, Italy

  2. 2

    University of Verona, Italy

Publication History

  1. Published Online: 27 JAN 2005
  2. Published Print: 11 FEB 2005

ISBN Information

Print ISBN: 9780471648178

Online ISBN: 9780471709152



  • Ionization of macromolecules;
  • electrospray;
  • matrix assisted laser desorption ionization (MALDI);
  • 252Cf plasma desorption;
  • fast atom/ion bombardment;
  • micro-channel plates (MCPs);
  • cryogenic detectors;
  • desorption ionization on silicon (DIOS);
  • tandem mass spectrometry;
  • post source decay;
  • collision induced dissociation;
  • quadrupole-time-of-flight;
  • linear trap;
  • Fourier transform ion resonance (FT-ICR);
  • peptide sequencing;
  • database search;
  • peptide mass fingerprinting (PMF);
  • ion mobility mass spectrometry;
  • multidimensional chromatography;
  • superconducting tunnel junction (STJ);
  • normalconductor-insulator-superconductor (NIS);
  • hybrid analyzers;
  • MS-based proteomics;
  • human proteome organization (HUPO)


Mass spectrometry is one of the core components of modern proteomics. This central role is the direct result of continuous development and automation which mass spectrometry has experienced particularly over the last twenty years. The two ionization methods, ESI and MALDI together with two earlier ionization methods, FAB and 252Cf PD are described in some details. It has to be pointed out that on the instrumentation side there are a number of aspects, which are given a particular attention:

• Ion analysis is one component, which has experienced the major development over the last 20 years. Such development has resulted in a number of new analyzers, which are playing a central role in today's proteomics. Among the emerging configurations described in this chapter are MALDI-TOF-TOF, linear ion trap-FT-ICR, and ion mobility-TOF. As well as these emerging configurations, an ample coverage of the well-established mass spectrometers such as the triple quadrupole, 3-D ion trap and quadrupole-TOF is also given.

• On the detection side, the authors discuss the advantages and limitations of micro-channel plates (MCPs), which are still the favorite detectors for commercial mass spectrometers. The need to improve the performance of these detectors to meet emerging needs in proteomics is underlined. A detailed discussion of cryogenic detectors both superconducting tunnel junction and thermal and their possible use as an alternative to MCPs is also given.

• The use of different MS data to search databases is another topic covered in this chapter. These data include MS-MS data generated by collision induced dissociation, peptide mass finger printing and post source decay. The capability of MALDI-TOF-TOF to generate high collision energy data and its influence on the accuracy of the search is also underlined.

• The increasing use of multi-dimensional chromatography in conjunction with various MS configurations and its contribution to high throughput proteomic analysis is discussed. The advantages and limitations of this approach and its comparison with gel-based separation are also highlighted.