Elsevier

Journal of Proteomics

Volume 73, Issue 11, 10 October 2010, Pages 2064-2077
Journal of Proteomics

Review
Two-dimensional gel electrophoresis in proteomics: Past, present and future

https://doi.org/10.1016/j.jprot.2010.05.016Get rights and content

Abstract

Two-dimensional gel electrophoresis has been instrumental in the birth and developments of proteomics, although it is no longer the exclusive separation tool used in the field of proteomics. In this review, a historical perspective is made, starting from the days where two-dimensional gels were used and the word proteomics did not even exist. The events that have led to the birth of proteomics are also recalled, ending with a description of the now well-known limitations of two-dimensional gels in proteomics. However, the often-underestimated advantages of two-dimensional gels are also underlined, leading to a description of how and when to use two-dimensional gels for the best in a proteomics approach. Taking support of these advantages (robustness, resolution, and ability to separate entire, intact proteins), possible future applications of this technique in proteomics are also mentioned.

Graphical abstract

This review article starts with the birth of 2D electrophoresis, investigates how it has been instrumental to the birth of proteomics, and examines its position in the current proteomics landscape.

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Section snippets

From mute star maps to protein buzz: two-dimensional electrophoresis and the birth of proteomics

SDS electrophoresis in its modern form was introduced in the early 70s [1] and soon became very widely used by protein biochemists. However, analysis of complex cellular extracts by this method made obvious the fact that the resolution was far from being sufficient to separate the many protein components of such extracts. To increase the resolution to a sufficient extent, it was necessary to couple two independent separations. At that time (and this is still the case) it was obvious that the

The take-off of proteomics

This possibility to be able to analyze spot of interest coming from 2D gels was a crucial change of paradigm, and the real start of proteomics. At those times where no complete genome was published yet, Edman sequencing provided enough information to look for homologs, or to devise oligonucleotides for screening DNA libraries. It was also the starting of brief golden age of 2D gel images databases [43], [44], [45], [46], [47]. To be useful to the community, 2D gel image databases must contain

Touching the limits of 2D electrophoresis, and the creation of alternate methods

Because of this intensive and worldwide effort using 2D electrophoresis and mass spectrometry as the core tool, many data were accumulated and analyzed, and it soon became obvious that it was always the same types of proteins that were found again and again, and the same types that were always missing, i.e. the low abundance and the hydrophobic proteins [61], [62].

In order to improve the resolution of hydrophobic proteins, many efforts were devoted to improve protein solubilization under the

Using the strengths of 2D gels in modern proteomic research

In this section, we will try to sort out the major strengths of 2D gels and to exemplify how they can be used for the benefit of proteomic research.

Concluding remarks. What future for 2D gels in proteomics

From all of the above, it is tempting to try to predict the future uses of 2D electrophoresis in the future, although this prediction exercise is always difficult and risky. It can be analyzed, however, that in the present proteomics landscape, 2D electrophoresis has two main drawbacks and three main advantages. The two main drawbacks are its very low efficiency (to say the least), in the analysis of hydrophobic proteins, and its high sensitivity to the dynamic range and quantitative

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