Comparative metabolomics with Metaboseek reveals functions of a conserved fat metabolism pathway in C. elegans

Abstract

Untargeted metabolomics via high-resolution mass spectrometry (HRMS) can reveal more than 100,000 molecular features in a single sample, many of which may represent unidentified metabolites, posing significant challenges to data analysis. We here introduce Metaboseek, an open-source analysis platform designed for untargeted comparative metabolomics and demonstrate its utility by uncovering biosynthetic functions of a conserved fat metabolism pathway, -oxidation, using C. elegans as a model. Metaboseek integrates modules for molecular feature detection, statistics, molecular formula prediction, and fragmentation (MS/MS) analysis, which uncovered more than 200 previously uncharacterized -oxidation-dependent metabolites in an untargeted comparison of wildtype and -oxidation-defective hacl-1 mutants. The identified metabolites support the predicted enzymatic function of HACL-1 and revealed that -oxidation participates in metabolism of endogenous {beta}-methyl-branched fatty acids and food-derived cyclopropane lipids. Our results showcase compound discovery and feature annotation at scale via untargeted comparative metabolomics applied to a conserved primary metabolic pathway and suggest a model for the metabolism of cyclopropane lipids.