Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.
Nucleic Acids Res. 2017 Jul 3;45(W1):W276-W284. doi: 10.1093/nar/gkx411.
The molecular understanding of cellular processes requires the identification and characterization of the involved protein complexes. Affinity-purification and mass spectrometric analysis (AP-MS) are performed on a routine basis to detect proteins assembled in complexes. In particular, protein abundances obtained by quantitative mass spectrometry and direct protein contacts detected by crosslinking and mass spectrometry (XL-MS) provide complementary datasets for revealing the composition, topology and interactions of modules in a protein network. Here, we aim to combine quantitative and connectivity information by a webserver tool in order to infer protein complexes. In a first step, modeling protein abundances and functional annotations from Gene Ontology (GO) results in a network which, in a second step, is integrated with connectivity data from XL-MS analysis in order to complement and validate the protein complexes in the network. The output of our integrative approach is a quantitative protein interaction map which is supplemented with topological information of the detected protein complexes. compleXView is built up by two independent modules which are dedicated to the analysis of label-free AP-MS data and to the visualization of the detected complexes in a network together with crosslink-derived distance restraints. compleXView is available to all users without login requirements at http://xvis.genzentrum.lmu.de/compleXView.
细胞过程的分子理解需要鉴定和描述涉及的蛋白质复合物。亲和纯化和质谱分析（AP-MS）是常规进行的，以检测组装在复合物中的蛋白质。特别是，通过定量质谱获得的蛋白质丰度和通过交联和质谱（XL-MS）检测到的直接蛋白质接触提供了互补的数据集，用于揭示蛋白质网络中模块的组成、拓扑结构和相互作用。在这里，我们旨在通过网络服务器工具结合定量和连接信息，以推断蛋白质复合物。在第一步中，我们将蛋白质丰度和功能注释建模为基因本体论（GO）结果的网络，在第二步中，将其与 XL-MS 分析的连接数据集成，以补充和验证网络中的蛋白质复合物。我们的综合方法的输出是一个定量蛋白质相互作用图，其中补充了检测到的蛋白质复合物的拓扑信息。 compleXView 由两个独立的模块组成，分别用于分析无标签的 AP-MS 数据和在网络中可视化检测到的复合物，并与交联衍生的距离约束一起使用。 compleXView 可供所有用户使用，无需登录要求，网址为 http://xvis.genzentrum.lmu.de/compleXView。
