FERMO: a Dashboard for Automated Prioritization of Molecular Features from Mass Spectral Data

Mitja M Zdouc, Hannah E Augustijn, Nataliia V Machushynets, Lina M Bayona, Sylvia Soldatou, Niek F de Jonge, Sarah Casu, Marcel Jaspars, Gilles P van Wezel, Marnix H Medema, Justin JJ van der Hooft

Abstract: Small molecules shape phenotypic variation by modulating biological processes, yet linking specific molecules to observed traits remains challenging due to the complexity of biological samples. Liquid chromatography-tandem mass spectrometry routinely detects hundreds of molecules per sample, and computational tools aid in the selection of the biologically relevant subset by organizing, annotating, and integrating orthogonal data. Existing tools typically focus on facilitating data-driven exploration to support manual interpretation, rather than more objective, data-driven prioritization and hypothesis-generation. Here, we introduce FERMO, a free online dashboard interface for prioritization of molecular features and samples associated with phenotypes of interest. FERMO’s modular framework automates data processing, annotation, and integration of standardized phenotypic and other metadata. FERMO supports both exploratory and targeted analysis through efficient interactive visualization, reproducible prioritization, and data filtering. We demonstrate FERMO’s utility in benchmarking studies prioritizing bioactive compounds from complex biological matrices. FERMO is freely available at https://fermo.bioinformatics.nl/.