Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
J Proteomics. 2013 Aug 2;88:4-13. doi: 10.1016/j.jprot.2013.01.010. Epub 2013 Jan 24.
With the rapid advance of MS-based proteomics one might think that 2D gel-based proteomics is dead. This is far from the truth. Current research has shown that there are still a number of places in the field of protein and molecular biology where 2D gels still play a leading role. The aim of this review is to highlight some of these applications. Examples from our own research as well as from other published works are used to illustrate the 2D gel driven research in the areas of: 1) de novo sequencing and protein identification from organisms with no or incomplete genome sequences available; 2) alternative detection methods for modification specific proteomics; 3) identification of protein isoforms and modified proteins. With an example of the glycoprotein TIMP-1 protein we illustrate the unique properties of 2D gels for the separation and characterisation of multiply modified proteins. We also show that careful analysis of experimental and theoretical protein mass and pI can lead to the identification of unanticipated protein variants modified by for example proteolytic cleavage. Together this shows that there is an important niche for 2D gel-based proteomics, which compliments traditional LC-MS techniques for specific protein research purposes.
随着基于 MS 的蛋白质组学的快速发展，人们可能认为基于 2D 凝胶的蛋白质组学已经过时了。但事实远非如此。目前的研究表明，在蛋白质和分子生物学领域，仍有许多地方需要 2D 凝胶来发挥主导作用。本文旨在强调其中的一些应用。本文使用了来自我们自己的研究和其他已发表的工作的例子来说明 2D 凝胶在以下领域的驱动研究：1）从头测序和无可用或不完全基因组序列的生物体的蛋白质鉴定；2）修饰特异性蛋白质组学的替代检测方法；3）鉴定蛋白质同工型和修饰蛋白质。我们以糖蛋白 TIMP-1 蛋白为例，说明了 2D 凝胶在分离和表征多修饰蛋白方面的独特性质。我们还表明，仔细分析实验和理论蛋白质质量和 pI 可以导致鉴定出未预期的被例如蛋白水解切割修饰的蛋白质变体。综上所述，2D 凝胶蛋白质组学有一个重要的利基市场，它可以补充传统的 LC-MS 技术，用于特定的蛋白质研究目的。
