Structure-centric searching enables global mapping of the public metabolome.

El Abiead, Yasin; Seo, Jeong In; Charron-Lamoureux, Vincent; Strobel, Michael; Gonçalves Nunes, Wilhan Donizete; Zhao, Haoqi Nina; Kvitne, Kine Eide; Zuffa, Simone et al. · Nat Biotechnol · 2026

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Abstract

Searching and learning from aggregated public metabolomics data spanning thousands of studies remained largely inaccessible. Here we present StructureMASST, a web-based application enabling scalable, structure-centric searches across public metabolomics repositories using molecule names or chemical representations. It queries a precomputed knowledgebase of 2.19 billion spectral matches and 420 million metadata links, supports modification-tolerant and mass-shift searches, and maps chemical structures across taxonomy, biological context and environmental conditions to accelerate discovery.