Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.
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DOI：
10.1002/0471250953.bi0815s39
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发表时间：
2012-09
影响因子：
--
通讯作者：
Nesvizhskii, Alexey I
中科院分区：
文献类型：
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作者：
Choi, Hyungwon;Liu, Guomin;Mellacheruvu, Dattatreya;Tyers, Mike;Gingras, Anne-Claude;Nesvizhskii, Alexey I
INTeractome的显著性分析（SAINT）是一个软件包，用于在亲和纯化-质谱（AP-MS）实验中基于无标记的定量蛋白质组学数据（如光谱计数或强度）对蛋白质-蛋白质相互作用进行评分。SAINT允许工作台科学家以公正的方式选择真正的相互作用并去除非特定的相互作用。然而，没有一个“放之四海而皆准”的统计模型适用于每个数据集，因为不同研究的实验设计各不相同。关键变量包括诱饵数量、每个诱饵的生物重复数量和对照纯化。在这里，我们详细介绍了输入数据格式、控制数据、高置信度交互的选择以及过滤数据的可视化。我们解释了用于定制统计模型的其他选项，以便在特定数据集中进行最佳过滤。我们还讨论了与LIMS系统ProHits连接的SAINT的图形用户界面，该界面可以作为虚拟机安装在Mac OSX或PC Windows计算机上。
Significance Analysis of INTeractome (SAINT) is a software package for scoring protein-protein interactions based on label-free quantitative proteomics data (e.g. spectral count or intensity) in affinity purification – mass spectrometry (AP-MS) experiments. SAINT allows bench scientists to select bona fide interactions and remove non-specific interactions in an unbiased manner. However, there is no `one-size-fits-all' statistical model for every dataset, since the experimental design varies across studies. Key variables include the number of baits, the number of biological replicates per bait, and control purifications. Here we give a detailed account of input data format, control data, selection of high confidence interactions, and visualization of filtered data. We explain additional options for customizing the statistical model for optimal filtering in specific datasets. We also discuss a graphical user interface of SAINT in connection to the LIMS system ProHits which can be installed as a virtual machine on Mac OSX or PC Windows computers.