Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
Semin Cell Dev Biol. 2012 Oct;23(8):863-71. doi: 10.1016/j.semcdb.2012.05.006. Epub 2012 Jun 5.
Reversible protein phosphorylation is involved in the regulation of most, if not all, major cellular processes via dynamic signal transduction pathways. During the last decade quantitative phosphoproteomics have evolved from a highly specialized area to a powerful and versatile platform for analyzing protein phosphorylation at a system-wide scale and has become the intuitive strategy for comprehensive characterization of signaling networks. Contemporary phosphoproteomics use highly optimized procedures for sample preparation, mass spectrometry and data analysis algorithms to identify and quantify thousands of phosphorylations, thus providing extensive overviews of the cellular signaling networks. As a result of these developments quantitative phosphoproteomics have been applied to study processes as diverse as immunology, stem cell biology and DNA damage. Here we review the developments in phosphoproteomics technology that have facilitated the application of phosphoproteomics to signaling networks and introduce examples of recent system-wide applications of quantitative phosphoproteomics. Despite the great advances in phosphoproteomics technology there are still several outstanding issues and we provide here our outlook on the current limitations and challenges in the field.
蛋白质可逆磷酸化通过动态信号转导途径参与大多数（如果不是全部的话）主要细胞过程的调节。在过去的十年中，定量磷酸蛋白质组学已经从一个高度专业化的领域发展成为一个用于在系统范围内分析蛋白质磷酸化的强大而通用的平台，并已成为全面描述信号网络的直观策略。当代磷酸蛋白质组学使用经过高度优化的样品制备、质谱和数据分析算法程序来鉴定和定量数千种磷酸化，从而提供对细胞信号网络的广泛概述。由于这些发展，定量磷酸蛋白质组学已被应用于研究免疫学、干细胞生物学和 DNA 损伤等多种过程。在这里，我们回顾了促进磷酸蛋白质组学在信号网络中应用的磷酸蛋白质组学技术的发展，并介绍了定量磷酸蛋白质组学的最新系统范围应用的实例。尽管磷酸蛋白质组学技术取得了巨大进展，但仍存在一些悬而未决的问题，我们在此提供了对该领域当前限制和挑战的看法。
