Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
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DOI：
10.1038/nature04670
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发表时间：
2006-03-30
期刊：
影响因子：
64.8
通讯作者：
Greenblatt, JF
中科院分区：
文献类型：
--
作者：
Krogan, NJ;Cagney, G;Greenblatt, JF
蛋白质-蛋白质相互作用的鉴定通常提供对蛋白质功能的洞察，并且许多细胞过程由稳定的蛋白质复合物执行。我们使用串联亲和纯化来处理酿酒酵母的4，562种不同标记的蛋白质。通过基质辅助激光解吸/电离-飞行时间质谱法和液相色谱串联质谱法分析每种制剂，以增加覆盖率和准确度。使用机器学习来整合质谱评分并将概率分配给蛋白质-蛋白质相互作用。在通过质谱法从2，357个成功纯化中以高置信度鉴定的4，087种不同蛋白质中，我们的核心数据集（中值精度为0.69）包括7，123种蛋白质-蛋白质相互作用，涉及2，708种蛋白质。马尔可夫聚类算法将这些相互作用组织成547个蛋白质复合物，平均每个复合物4.9个亚基，其中约一半在MIPS数据库中缺失，以及复合物对之间的429个额外相互作用。这些数据（所有这些都可以在线获得）将有助于未来对单个蛋白质以及功能基因组学和系统生物学的研究。
Identification of protein - protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ ionization - time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein - protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set ( median precision of 0.69) comprises 7,123 protein - protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data ( all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.