Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital.
Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital.
J Vis Exp. 2021 Oct 19(176). doi: 10.3791/62796.
With recent advances in mass spectrometry-based proteomics technologies, deep profiling of hundreds of proteomes has become increasingly feasible. However, deriving biological insights from such valuable datasets is challenging. Here we introduce a systems biology-based software JUMPn, and its associated protocol to organize the proteome into protein co-expression clusters across samples and protein-protein interaction (PPI) networks connected by modules (e.g., protein complexes). Using the R/Shiny platform, the JUMPn software streamlines the analysis of co-expression clustering, pathway enrichment, and PPI module detection, with integrated data visualization and a user-friendly interface. The main steps of the protocol include installation of the JUMPn software, the definition of differentially expressed proteins or the (dys)regulated proteome, determination of meaningful co-expression clusters and PPI modules, and result visualization. While the protocol is demonstrated using an isobaric labeling-based proteome profile, JUMPn is generally applicable to a wide range of quantitative datasets (e.g., label-free proteomics). The JUMPn software and protocol thus provide a powerful tool to facilitate biological interpretation in quantitative proteomics.
随着基于质谱的蛋白质组学技术的最新进展，深度分析数百种蛋白质组变得越来越可行。然而，从这些有价值的数据集得出生物学见解具有挑战性。在这里，我们介绍了一种基于系统生物学的软件 JUMPn 及其相关协议，用于将蛋白质组组织成跨样本的蛋白质共表达簇和由模块（例如蛋白质复合物）连接的蛋白质-蛋白质相互作用 (PPI) 网络。使用 R/Shiny 平台，JUMPn 软件简化了共表达聚类、途径富集和 PPI 模块检测的分析，具有集成的数据可视化和用户友好的界面。该协议的主要步骤包括 JUMPn 软件的安装、差异表达蛋白或（失调）蛋白质组的定义、有意义的共表达簇和 PPI 模块的确定以及结果可视化。虽然该协议使用基于等压标记的蛋白质组谱进行了演示，但 JUMPn 通常适用于广泛的定量数据集（例如无标记蛋白质组学）。因此，JUMPn 软件和协议为定量蛋白质组学中的生物学解释提供了强大的工具。
