Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
Copyright policy )Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
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.
- University of Iceland Iceland
- University of Illinois at Chicago United States
- University of California, San Francisco United States
natural products, Bioinformatics, Bioengineering, Biochemistry, Microbiology, Lífefnafræði, Litrófsgreining, Bacterial Proteins, Matrix-Assisted Laser Desorption-Ionization, Psychology, MALDI-TOF MS, Cluster Analysis, Örverufræði, Natural products, Mass spectrometry, Spectrometry, specialized metabolites, microbiology, bioinformatics, Biological Sciences, Mass, Specialized metabolites, Opinn hugbúnaður, Issue 147, Biochemistry and cell biology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Metabolome, Cognitive Sciences, Biochemistry and Cell Biology, Software
natural products, Bioinformatics, Bioengineering, Biochemistry, Microbiology, Lífefnafræði, Litrófsgreining, Bacterial Proteins, Matrix-Assisted Laser Desorption-Ionization, Psychology, MALDI-TOF MS, Cluster Analysis, Örverufræði, Natural products, Mass spectrometry, Spectrometry, specialized metabolites, microbiology, bioinformatics, Biological Sciences, Mass, Specialized metabolites, Opinn hugbúnaður, Issue 147, Biochemistry and cell biology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Metabolome, Cognitive Sciences, Biochemistry and Cell Biology, Software
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