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J Vis Exp. 2019 May 15;(147). doi: 10.3791/59219.

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data.

Author information

1
Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago.
2
Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago; Faculty of Pharmaceutical Sciences, University of Iceland.
3
Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago; btmurphy@uic.edu.

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.

PMID:
31157770
DOI:
10.3791/59219

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