Code and knowledgebase data for "IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry"

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This repository contains the complete codebase and infrastructure for the IDBac platform, a centralized knowledgebase and analysis system for bacterial dereplication using MALDI-TOF mass spectrometry protein signatures.

Please note: While the current IDBac knowledgebase contains version 4.2 of the RKI database, the JSON file listed here intentionally excludes this. Please find the source data for RKI used in the publication here.

Abstract

The identification of bacteria is central to microbiological sciences. While gene sequencing methods have been the standard to identify bacteria, use of MALDI-TOF mass spectrometry (MS) in clinical microbiology provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical microbiology due to the lack of a centralized public database of MS protein signatures that would facilitate strain identification via spectral comparison. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures of >1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections, and visualize specialized metabolite differences within groups of closely related bacteria. We highlight this utility by demonstrating the dereplication of bacterial isolates using the seed knowledgebase, identifying trends in culture collections using metadata integration, and reporting the discovery of a new metabolite from a Paraburkholderia isolate.