Metaboolset

Metaboolset is a term used in metabolomics to denote a curated collection of metabolites that are grouped by shared pathway, function, or biological context. The term is not universally standardized and may be used variably in different sources; in many cases it is synonymous with metabolite sets or metabolite signatures used for pathway-level interpretation of metabolomics data.

A metaboolset typically comprises a list of metabolite identifiers (for example HMDB IDs, KEGG Compound IDs, ChEBI IDs) linked to curated annotations from databases such as KEGG, Reactome, HMDB. Sets range from a few dozen to hundreds of metabolites and may be restricted to a species or tissue type. They are used with enrichment- or overrepresentation-based analyses in which metabolomics data are tested for coordinated changes within a set, analogous to gene set enrichment analysis (GSEA) in transcriptomics. Software tools that perform metabolite set enrichment analysis rely on metaboolsets to map measured features to known biochemical contexts.

Applications include interpretation of LC-MS or NMR metabolomics, pathway activity inference, and biomarker discovery. In disease research, metaboolsets can help identify dysregulated pathways and generate mechanistic hypotheses. However, challenges include incomplete metabolite coverage across platforms, ambiguous identifications, isomer indistinguishability, and inconsistent naming across databases. Because metabolite annotation and cross-reference mapping vary, the reproducibility of metaboolset–based analyses depends on careful curation and use of standardized identifiers.

Related topics include metabolomics, metabolite set enrichment analysis, KEGG, HMDB, and Reactome.