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Updated: Aug 26, 2026

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
Published on: May 15, 2019
IDBac: an open-access web platform to identify bacteria and analyze relationships in culture collections using
Nyssa K Krull1, Michael Strobel2, Julia Saulog3
1Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, USA.
Abstract:
The identification and analysis of bacteria is central to the microbiological sciences. While gene sequencing methods have been the standard to achieve this, use of MALDI-TOF mass spectrometry (MS), particularly in clinical microbiology, can provide high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical settings due to the lack of a centralized public database of MS protein signatures that would facilitate isolate identification via spectral comparison. Further, most current MALDI MS data analysis platforms lack meaningful ways to compare properties from large numbers of bacterial isolates. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures spanning seven bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections using metadata integration, and visualize specialized metabolite differences within groups of closely related bacteria. To highlight this utility and encourage wide community contribution, examples of each are presented.
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