Zhan Xianquan, Li Biao, Zhan Xiaohan, Schlüter Hartmut, Jungblut Peter R, Coorssen Jens R
Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, 87 Xiangya Road, Changsha 410008, China.
Hunan Engineering Laboratory for Structural Biology and Drug Design, Central South University, 87 Xiangya Road, Changsha 410008, China.
Proteomes. 2019 Oct 30;7(4):36. doi: 10.3390/proteomes7040036.
Two-dimensional gel electrophoresis (2DE) is an important and well-established technical platform enabling extensive top-down proteomic analysis. However, the long-held but now largely outdated conventional concepts of 2DE have clearly impacted its application to in-depth investigations of proteomes at the level of protein species/proteoforms. It is time to popularize a new concept of 2DE for proteomics. With the development and enrichment of the proteome concept, any given "protein" is now recognized to consist of a series of proteoforms. Thus, it is the proteoform, rather than the canonical protein, that is the basic unit of a proteome, and each proteoform has a specific isoelectric point (p) and relative mass (). Accordingly, using 2DE, each proteoform can routinely be resolved and arrayed according to its different p and . Each detectable spot contains multiple proteoforms derived from the same gene, as well as from different genes. Proteoforms derived from the same gene are distributed into different spots in a 2DE pattern. High-resolution 2DE is thus actually an initial level of separation to address proteome complexity and is effectively a pre-fractionation method prior to analysis using mass spectrometry (MS). Furthermore, stable isotope-labeled 2DE coupled with high-sensitivity liquid chromatography-tandem MS (LC-MS/MS) has tremendous potential for the large-scale detection, identification, and quantification of the proteoforms that constitute proteomes.
二维凝胶电泳（2DE）是一个重要且成熟的技术平台，可实现广泛的自上而下的蛋白质组学分析。然而，长期以来但现在已基本过时的2DE传统概念显然影响了其在蛋白质种类/蛋白质异构体水平上对蛋白质组进行深入研究的应用。现在是时候推广蛋白质组学中2DE的新概念了。随着蛋白质组概念的发展和丰富，现在人们认识到任何给定的“蛋白质”都由一系列蛋白质异构体组成。因此，蛋白质异构体而非标准蛋白质才是蛋白质组的基本单位，并且每个蛋白质异构体都有特定的等电点（p）和相对质量（）。相应地，使用2DE，每个蛋白质异构体都可以根据其不同的p和常规地进行分离和排列。每个可检测到的斑点都包含来自同一基因以及不同基因的多种蛋白质异构体。来自同一基因的蛋白质异构体在2DE图谱中分布在不同的斑点中。因此，高分辨率2DE实际上是解决蛋白质组复杂性的初始分离水平，并且实际上是在使用质谱（MS）分析之前的预分级方法。此外，稳定同位素标记的2DE与高灵敏度液相色谱 - 串联质谱（LC-MS/MS）相结合，在大规模检测、鉴定和定量构成蛋白质组的蛋白质异构体方面具有巨大潜力。
