An integrated mass spectrometric and computational framework for the analysis of protein interaction networks
An integrated mass spectrometric and computational framework for the analysis of protein interaction networks
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DOI：
10.1038/nbt1289
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发表时间：
2007-03-01
影响因子：
46.9
通讯作者：
Aebersold, Ruedi
中科院分区：
文献类型：
--
作者：
Rinner, Oliver;Mueller, Lukas N.;Aebersold, Ruedi
生物系统由蛋白质复合物控制，蛋白质复合物结合成动态蛋白质相互作用网络。我们描述了一种策略，分析蛋白质复合物，通过整合无标记，定量质谱和计算分析。通过评估整个样品顺序稀释过程中的肽强度分布，MasterMap系统可识别特定的相互作用伙伴，检测蛋白质复合物组成的变化，并揭示蛋白质复合物组分磷酸化状态的变化。我们使用含有人类叉头转录因子FoxO 3A的复合物来证明该技术的有效性和性能。我们的分析确定了以前已知的和未知的FoxO 3A与14-3-3蛋白的相互作用，除了确定FoxO 3A磷酸化位点和检测磷酸肌醇-3激酶抑制后减少的14-3-3结合。通过提高相互作用网络的特异性和灵敏度，评估翻译后修饰和提供动态相互作用谱，MasterMap系统解决了目前蛋白质复合物方法的几个局限性。
Biological systems are controlled by protein complexes that associate into dynamic protein interaction networks. We describe a strategy that analyzes protein complexes through the integration of label-free, quantitative mass spectrometry and computational analysis. By evaluating peptide intensity profiles throughout the sequential dilution of samples, the MasterMap system identifies specific interaction partners, detects changes in the composition of protein complexes and reveals variations in the phosphorylation states of components of protein complexes. We use the complexes containing the human forkhead transcription factor FoxO3A to demonstrate the validity and performance of this technology. Our analysis identifies previously known and unknown interactions of FoxO3A with 14-3-3 proteins, in addition to identifying FoxO3A phosphorylation sites and detecting reduced 14-3-3 binding following inhibition of phosphoinositide-3 kinase. By improving specificity and sensitivity of interaction networks, assessing post-translational modifications and providing dynamic interaction profiles, the MasterMap system addresses several limitations of current approaches for protein complexes.