Work

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

Year: 2019

Type: article

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.

Source: Journal of Visualized Experiments

DOI: 10.3791/59219

Authors: Chase M. Clark, Maria S. Costa, Erin Conley, Emma Li, Laura M. Sanchez, Brian T. Murphy

Institutions: University of Illinois Chicago, University of Iceland

Language: English

Topic: Bacterial Identification and Susceptibility Testing

Subfield: Clinical Biochemistry

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Geographic Society, University of Illinois at Urbana-Champaign, National Institute of General Medical Sciences, National Center for Complementary and Integrative Health

Awards: A new paradigm for the creation and mining of microbial libraries for drug discovery, G5228372456, A New Paradigm in Developing Microbial Libraries for Drug Discovery