Overview
IDBac combines bacterial MALDI protein fingerprints with specialized-metabolite profiles to compare cultured isolates. Its web platform provides reference matching, protein-similarity views and metabolite-association analysis. This entry covers the current platform and its earlier R/desktop methods; older installation instructions are not interchangeable with the current GNPS2 interface.
What can this tool do?
Common uses
- Compare specialized-metabolite profiles among related bacterial isolates.
- Prioritize culture-collection isolates for follow-up MS analysis.
Scientific fit
Primary function
Reference data and database search
Other functions
Molecular networking and chemical similarity, Visualization and reporting, Data management and sharing
Analysis types
Metabolite profiling
Data compatibility
Inputs
Mass spectra, Sample metadata
Outputs
Mass spectra, Statistical results, Human-readable report
Input formats
mzML, CSV or TSV, MALDI protein and specialized-metabolite spectra with plate-map metadata
Output formats
CSV or TSV, Protein dendrograms and heatmaps, Metabolite association networks and analysis tables
Scope and considerations
Designed for
- High-throughput analysis of cultured bacterial isolates using MALDI-TOF or compatible MALDI mass-spectrometry data.
- Connecting taxonomic or protein-fingerprint similarity with differences in specialized-metabolite production.
- Culture-collection dereplication and strain prioritization before labor-intensive scale-up.
Not designed for
- Replacing sequence-based taxonomy when definitive taxonomic resolution is required.
- Complete structural elucidation of specialized metabolites from MALDI-MS1 profiles alone.
Important requirements
- Reproducible MALDI sample preparation and appropriate replicate acquisition.
- Protein-region spectra for bacterial grouping or identification and, where chemical comparison is desired, lower-mass specialized-metabolite spectra.
Considerations
- Protein spectral similarity is not definitive sequence-based taxonomy.
- Culture conditions, MALDI matrix and acquisition settings affect detected chemical profiles.
- MS1 metabolite-association networks do not establish structures or imply MS/MS fragmentation similarity.
Access and documentation
The account-request documentation requires a GNPS2 account requested through an academic affiliation and describes a staged closed-beta rollout. Check the current request page before planning an analysis. Public reference or example views do not establish unrestricted analysis access.
Evidence and review
Official project documentation and direct tool publication metadata reviewed on 2026-09-12. No account creation, data upload, installation or independent benchmarking performed. Included for MALDI specialized-metabolite profiling and culture-collection interpretation. The separate colony MALDI-MS/MS method paper is not listed as a core platform publication.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Clark CM, Costa MS, Sanchez LM, Murphy BT. Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function. Proceedings of the National Academy of Sciences 115, 4981-4986 (2018). doi:10.1073/pnas.1801247115 PMID 29686101
- Clark CM, Costa MS, Conley E, Li E, Sanchez LM, Murphy BT. Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data. Journal of Visualized Experiments 147, e59219 (2019). doi:10.3791/59219 PMID 31157770
- Clark CM, Nguyen L, Pham VC, et al. Automated Microbial Library Generation Using the Bioinformatics Platform IDBac. Molecules 27, 2038 (2022). doi:10.3390/molecules27072038 PMID 35408437
- Krull NK, Strobel M, Saulog J, et al. IDBac: an open-access web platform to identify bacteria and analyze relationships in culture collections using MALDI-TOF mass spectrometry. Nature Communications 17, 8956 (2026). doi:10.1038/s41467-026-75579-4 PMID 42637730
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-12 · First committed entry
Add IDBac and RaMP specialist resources
View change · Entry at this revision