使用开源基质辅助激光解吸电离飞行时间质谱微生物鉴定数据库管道分析微生物蛋白质和特殊代谢物数据。
Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data.
作者信息
Clark Chase M, Costa Maria S, Conley Erin, Li Emma, Sanchez Laura M, Murphy Brian T
机构信息
Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago.
Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago; Faculty of Pharmaceutical Sciences, University of Iceland.
出版信息
J Vis Exp. 2019 May 15(147). doi: 10.3791/59219.
Abstract
In order to visualize the relationship between bacterial phylogeny and specialized metabolite production of bacterial colonies growing on nutrient agar, we developed IDBac-a low-cost and high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bioinformatics pipeline. IDBac software is designed for non-experts, is freely available, and capable of analyzing a few to thousands of bacterial colonies. Here, we present procedures for the preparation of bacterial colonies for MALDI-TOF MS analysis, MS instrument operation, and data processing and visualization in IDBac. In particular, we instruct users how to cluster bacteria into dendrograms based on protein MS fingerprints and interactively create Metabolite Association Networks (MANs) from specialized metabolite data.
摘要
为了可视化在营养琼脂上生长的细菌菌落的系统发育与特殊代谢产物产生之间的关系，我们开发了IDBac——一种低成本、高通量的基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF MS）生物信息学流程。IDBac软件是为非专业人员设计的，可免费获取，并且能够分析少量到数千个细菌菌落。在此，我们介绍用于MALDI-TOF MS分析的细菌菌落制备、质谱仪操作以及IDBac中的数据处理和可视化的流程。特别是，我们指导用户如何根据蛋白质质谱指纹将细菌聚类成树状图，并根据特殊代谢产物数据交互式创建代谢产物关联网络（MANs）。
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