Home › Microbiology › Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
Microbiology JoVE (Open Access) Citable · DOI

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

DOI: 10.3791/59219-v
What you'll learn
  • ✓ Prepare MALDI target plates and acquire spectra
  • ✓ Install IDBac and import raw data
  • ✓ Analyze protein data and build dendrograms
  • ✓ Analyze specialized metabolites with association networks
Protocol

Biopharma Insights 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.

Difficulty
intermediate
Total time
~3-4 hrs/sample set
Biosafety
BSL-1

Steps

1
Prepare MALDI target plates and acquire data

Scrape bacterial colonies onto MALDI target plates, apply matrix, and acquire intact protein and specialized metabolite mass spectra.

▶ 01:10
2
Install IDBac and load raw data

Install the IDBac software and import the raw mass spectrometry data files into the pipeline.

▶ 02:02
3
Work with previous experiments

Open and manage previously saved IDBac experiments to continue analysis or compare data.

▶ 02:47
4
Set up protein analysis and create mirror plots

Configure protein data analysis parameters and generate mirror plots to compare spectra between samples.

▶ 03:22
5
Cluster samples using protein data

Perform hierarchical clustering based on intact protein spectra to group bacterial colonies into putative taxonomic groups.

▶ 04:07
6
Customize dendrogram and insert external samples

Customize the protein dendrogram appearance and insert samples from a separate experiment into the existing dendrogram for comparison.

▶ 04:49
7
Analyze specialized metabolite data and networks

Analyze specialized metabolite spectra and generate metabolite association networks (MANs) to differentiate colonies based on metabolite production.

▶ 05:32
8
Review results of IDBac analysis

Inspect the combined results from protein clustering and specialized metabolite networks to interpret taxonomic and metabolic relationships.

▶ 06:51
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