What does this strategy enable?
This strategy extends colony-level IDBac screening beyond MALDI-MS1 chemical fingerprints. Protein and specialized-metabolite MS1 data are first used to understand isolate identity and metabolite-production potential. Selected precursor ions are then fragmented by MALDI-MS/MS, and the resulting spectra are passed to GNPS2 for molecular networking and library searching. The layered workflow adds preliminary structural context early enough to influence which strains are advanced to scale-up.
Transferable workflow
Workflow
- 1
Profile colonies by MALDI-MS1
Acquire protein-region and specialized-metabolite spectra directly from microbial colonies and inspect the collection in IDBac.
- 2
Select small-molecule precursors for fragmentation
Use the colony-level specialized-metabolite data to choose precursor ions for MALDI tandem-MS acquisition while filtering matrix/background signals.
- 3
Acquire MALDI-MS/MS spectra
Fragment selected precursor ions directly from colony-derived samples to generate tandem spectra before fermentation scale-up.
- 4
Run downstream GNPS2 molecular networking
Submit compatible MALDI-MS/MS spectra to GNPS2 for molecular networking and spectral-library searching.
- 5
Prioritize strains and chemistry
Combine colony identity, metabolite-production patterns, molecular-family context, and preliminary annotations to select strains and compounds for scale-up and orthogonal structural validation.
Connected resources
Tools used in this strategy
Strategy profile
Related objectives
Dereplication, Molecular-family discovery, Metabolite annotation
Components
Sample preparation, Data acquisition, Preprocessing and feature extraction, Spectral search, Molecular networking, Annotation or identification, Biological validation
Sample types
Microbial culture or biomass
Biological context
Microbial
Ion mobility
Ion mobility not required
Scope and considerations
Designed for
- Early dereplication and strain prioritization in microbial natural-product discovery before large-scale fermentation and extraction.
- Linking colony-level metabolite production to MS/MS molecular families and tentative annotations.
Important requirements
- MALDI instrumentation capable of the required MS1 and tandem-MS acquisition workflow.
- Cultured microbial colonies and compatible IDBac/GNPS2 data preparation.
Considerations
- Colony-level production can differ from larger-scale fermentation, so prioritized chemistry should be reconfirmed after scale-up.
- Spectral-library matches and molecular-network relationships provide dereplication evidence but do not replace full structure elucidation.
Reusable resources
Publication
Shepherd RA, Gad LY, Strobel M, et al. MALDI Tandem Mass Spectrometry for Colony-Based Dereplication of Natural Products. Journal of Natural Products (2026).