A curated list of computational tools, databases, and software for metabolomics research published between 2021-2025.

Methodology We compiled this comprehensive list of computational tools and databases through a systematic approach. We began with manual curation of published metabolomics resources starting in 2021, building upon our prior review efforts (Misra, 2021; Misra and van der Hooft, 2015). To ensure complete coverage and minimize gaps, we subsequently employed three complementary strategies: Computational screening: Used AI-assisted tools and Google Scholar to identify emerging metabolomics software and databases across the 2021–2025 period Literature review: Systematically examined citations and references in recent comprehensive metabolomics reviews for each functional category Field experts: Reviewed our compilation with domain experts across different metabolomics subdisciplines Details at https://github.com/enveda/computational-metabolomics-review/