Glatter Timo, Wepf Alexander, Aebersold Ruedi, Gstaiger Matthias
Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Mol Syst Biol. 2009;5:237. doi: 10.1038/msb.2008.75. Epub 2009 Jan 20.
Protein complexes represent major functional units for the execution of biological processes. Systematic affinity purification coupled with mass spectrometry (AP-MS) yielded a wealth of information on the compendium of protein complexes expressed in Saccharomyces cerevisiae. However, global AP-MS analysis of human protein complexes is hampered by the low throughput, sensitivity and data robustness of existing procedures, which limit its application for systems biology research. Here, we address these limitations by a novel integrated method, which we applied and benchmarked for the human protein phosphatase 2A system. We identified a total of 197 protein interactions with high reproducibility, showing the coexistence of distinct classes of phosphatase complexes that are linked to proteins implicated in mitosis, cell signalling, DNA damage control and more. These results show that the presented analytical process will substantially advance throughput and reproducibility in future systematic AP-MS studies on human protein complexes.
蛋白质复合物是执行生物过程的主要功能单元。系统亲和纯化结合质谱分析（AP-MS）产生了大量关于酿酒酵母中表达的蛋白质复合物的信息。然而，现有方法的低通量、低灵敏度和数据稳健性阻碍了对人类蛋白质复合物的全局AP-MS分析，限制了其在系统生物学研究中的应用。在这里，我们通过一种新颖的综合方法解决了这些限制，并将其应用于人类蛋白磷酸酶2A系统并进行了基准测试。我们总共鉴定出197种具有高重现性的蛋白质相互作用，表明不同类别的磷酸酶复合物与参与有丝分裂、细胞信号传导、DNA损伤控制等的蛋白质共存。这些结果表明，所提出的分析方法将在未来对人类蛋白质复合物的系统AP-MS研究中大幅提高通量和重现性。
