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Briefings in Functional Genomics Advance Access originally published online on February 3, 2006
Briefings in Functional Genomics 2006 4(4):295-320; doi:10.1093/bfgp/eli002
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© The Author 2006. Published by Oxford University Press. All rights reserved. For permissions please email: journals.permissions@oxfordjournals.org

Mass spectrometry technologies for proteomics

Benito Cañas, Daniel López-Ferrer, Antonio Ramos-Fernández, Emilio Camafeita and Enrique Calvo

Corresponding author. Benito Cañas Montalvo, Dpto. de Química Analítica, Facultad de C. Químicas, Universidad Complutens, E-28040, Madrid, Spain. Tel: +34 91 394 43 68; Fax: +34 91 394 43 29; E-mail: bcanasmo{at}quim.ucm.es

In the late 1980s, the advent of soft ionization techniques capable of generating stable gas phase ions from thermally unstable biomolecules, namely matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), laid the way for the development of a set of powerful alternatives to the traditional Edman chemistry for the structural characterization of peptides and proteins. The rapid protein identification capabilities that, coupled with two-dimensional gel electrophoresis, provided insights into all sorts of biological systems since the dawn of proteomics and have been exploited in the last few years for the development of more powerful and automatable gel-free strategies, mainly based on multidimensional chromatographic separations of peptides from proteolytic digests. In parallel to the evolution of ion sources, mass analysers and scan modes, the invention of new elegant biochemical strategies to fractionate or simplify highly complex mixtures, or to introduce isotopic labels in peptides in a variety of ways now makes also possible large-scale, high-coverage quantitative studies in a wide dynamic range. In this review, we provide the fundamental concepts of mass spectrometry (MS) and describe the technological progress of MS-based proteomics since its earliest days. Representative literature examples of their true power, either when employed as exploratory or as targeted techniques, is provided as well.

Keywords: proteomics, mass spectrometry, post-translational modifications, second generation proteomics


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