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

Abstract

Untargeted metabolomics via high-resolution mass spectrometry 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, α-oxidation, using C. elegans as a model. Metaboseek integrates modules for molecular feature detection, statistics, molecular formula prediction, and fragmentation analysis, which uncovers more than 200 previously uncharacterized α-oxidation-dependent metabolites in an untargeted comparison of wildtype and α-oxidation-defective hacl-1 mutants. The identified metabolites support the predicted enzymatic function of HACL-1 and reveal that α-oxidation participates in metabolism of endogenous β-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.

Copper starvation induces antimicrobial isocyanide integrated into two distinct biosynthetic pathways in fungi

“…The resulting tables of all detected features were then processed with the Metaboseek data explorer. To remove background-derived features, we first applied filters that only retained entries with a retention time window of 1 to 20 min and then applied maximum intensity (at least one repeat >10,000), and Peak Quality (>0.98) thresholds, as calculated by Metaboseek 10 . To select differential features, we applied a filter (using Metaboseek) to select entries with peak area ratios larger than 20 (upregulated by copper starvation in wildtype) or 5 (up in overexpression mutants compared to wild types).…”

“…To identify crm-derived metabolites, we started by comparing the metabolomes of wildtype (WT) A. fumigatus and a ΔcrmA deletion mutant grown under copper-limited and copper-replete conditions, given that crmA expression is strongly copper-dependent 3 . Metabolite extracts were analyzed by high-resolution HPLC-MS (HPLC-HRMS), and the resulting datasets were compared using the Metaboseek software platform 10 , which facilitates comparative analysis of HPLC-HRMS data from multiple different conditions. These comparative analyses revealed a large number of MS features upregulated under low copper conditions.…”

Host hepatic metabolism is modulated by gut microbiota-derived sphingolipids

“…Untargeted metabolomic analysis RAW files generated from HPLC-HRMS acquisitions were converted to mzXML files utilizing MSconvertGUI software (proteowizard.sourceforge.net). Differential metabolic features were determined by subjecting mzXML files to Metaboseek Software version 0.9.6 (metaboseek.com) (Helf et al, 2022) utilizing the XCMS package with all values set to default parameters which are as follows: Peak Detection: ppm 4, peakwidth 320, snthresh 3, prefilter 3100, fitgauss FALSE, integrate 1, firstBaselineCheck TRUE, noise 0, mzCenterFun wMean, mzdiff -0.005, workers 4. Peak filling: METABOSEEK, ppm_m 5, rtw 5, rtrange TRUE, areaMode FALSE.…”

Effect of Sports Energy Drink on Fat Metabolism and Weight Loss of College Students

“…e substrate cycle of fat synthesis and decomposition is often carried out in adipose tissue, and the direction of the cycle is regulated and controlled by whether the body needs fat energy [2]. When fat is needed for energy supply, the rate of fat mobilization is accelerated.…”