Liu Guomin, Zhang Jianping, Choi Hyungwon, Lambert Jean-Philippe, Srikumar Tharan, Larsen Brett, Nesvizhskii Alexey I, Raught Brian, Tyers Mike, Gingras Anne-Claude
Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Ontario, Canada.
Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
Curr Protoc Bioinformatics. 2012 Sep;Chapter 8:8.16.1-8.16.32. doi: 10.1002/0471250953.bi0816s39.
Affinity purification coupled with mass spectrometry (AP-MS) is a robust technique used to identify protein-protein interactions. With recent improvements in sample preparation, and dramatic advances in MS instrumentation speed and sensitivity, this technique is becoming more widely used throughout the scientific community. To meet the needs of research groups both large and small, we have developed software solutions for tracking, scoring and analyzing AP-MS data. Here, we provide details for the installation and utilization of ProHits, a Laboratory Information Management System designed specifically for AP-MS interaction proteomics. This protocol explains: (i) how to install the complete ProHits system, including modules for the management of mass spectrometry files and the analysis of interaction data, and (ii) alternative options for the use of pre-existing search results in simpler versions of ProHits, including a virtual machine implementation of our ProHits Lite software. We also describe how to use the main features of the software to analyze AP-MS data.
亲和纯化结合质谱分析（AP-MS）是一种用于鉴定蛋白质-蛋白质相互作用的强大技术。随着近期样品制备技术的改进以及质谱仪器在速度和灵敏度方面的巨大进步，该技术在整个科学界得到了更广泛的应用。为满足大小研究团队的需求，我们开发了用于跟踪、评分和分析AP-MS数据的软件解决方案。在此，我们详细介绍ProHits的安装和使用方法，ProHits是一款专门为AP-MS相互作用蛋白质组学设计的实验室信息管理系统。本方案解释了：（i）如何安装完整的ProHits系统，包括用于管理质谱文件和分析相互作用数据的模块，以及（ii）在更简化版本的ProHits中使用预先存在的搜索结果的替代选项，包括我们的ProHits Lite软件的虚拟机实现。我们还描述了如何使用该软件的主要功能来分析AP-MS数据。
