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生物化学
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Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
JoVE 杂志
生物化学
This content is Free Access.
JoVE 杂志 生物化学
Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

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

DOI:
10.3791/59219-v

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09:29 min

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May 15, 2019

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, , , , ,
1Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy,University of Illinois at Chicago, 2Faculty of Pharmaceutical Sciences,University of Iceland

Chapters

  • 00:04Title
  • 01:10Preparation of MALDI Target Plates and Data Acquisition
  • 02:02Installing the IDBac Software and Starting with Raw Data
  • 02:47Work with Previous Experiments
  • 03:22Setting up Protein Data Analysis and Creating Mirror Plots
  • 04:07Clustering Samples Using Protein Data
  • 04:49Customizing the Protein Dendrogram and Inserting Samples from a Separate Experiment into the Dendrogram
  • 05:32Analyzing Specialized Metabolite Data and Metabolite Association Networks (MANs)
  • 06:51Results: Analysis of Microbial Protein and Specialized Metabolite Data by IDBac
  • 08:28Conclusion

Summary

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IDBac is an open-source mass spectrometry-based bioinformatics pipeline that integrates data from both intact protein and specialized metabolite spectra, collected on cell material scraped from bacterial colonies. The pipeline allows researchers to rapidly organize hundreds to thousands of bacterial colonies into putative taxonomic groups, and further differentiate them based on specialized metabolite production.

Tags

Keywords: MALDI TOF-MSIDBacMicrobial ProteinSpecialized MetaboliteBacterial IdentificationSoftwareMass SpectrometryMALDI MatrixData AnalysisBacterial ColoniesProtein SpectraMetabolite SpectraData Processing

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