Leveraging open cheminformatics tools for non-targeted metabolomics analysis of C. elegans: a workflow comparison and application to strains related to xenobiotic metabolism and neurodegeneration

26 May 2025, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Caenorhabditis elegans (C. elegans) is a well-established nematode model for studying metabolism and neurodegenerative disorders, such as Alzheimer’s (AD) and Parkinson’s disease (PD). Non-targeted metabolomics via liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has proven useful for uncovering metabolic changes in biological systems. Here, we present workflows for C. elegans metabolomics, leveraging advanced open science tools. We compared two metabolite extraction methods: a monophasic extraction, which provided broader metabolite coverage in analyses conducted in hydrophilic interaction with positive polarity (HILIC POS), and a biphasic extraction, which yielded more features in reverse-phase C18 chromatography with negative polarity (RPLC NEG) analyses. Data were processed using patRoon, integrating IPO, XCMS, CAMERA, and MetFrag, which incorporated PubChemLite compounds and C. elegans-specific metabolites from an expanded WormJam database enhanced with PubChem and literature sources. MS-DIAL was also employed for data processing, allowing for expanded annotations with predicted spectra for the expanded WormJam metabolites calculated using CFM-ID. Significant metabolite differences were identified when comparing the Bristol (N2) wildtype strain with two knockout strains of xenobiotic-metabolizing enzymes and two transgenic strains related to neurodegenerative pathways. Pooled quality control (QC) samples for each strain ensured robust data quality and the detection of strain-related metabolites. Our study indicates the potential of non-targeted metabolomics for metabolite discovery employing open science tools in metabolomics studies of model organisms.

Keywords

Untargeted metabolomics
exposomics
CYP enzyme mutant
FMO enzyme mutant
SV2C expression
Tau aggregation

Supplementary materials

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Supplementary data 1
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Supplementary figures from S1 to S18. The description of each figure is reported in the first page of the file.
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Supplementary data 2
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For each significant compound annotated at level 3 or above, a boxplot shows the distribution in the considered groups of strains.
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Supplementary tables
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Supplementary tables from S1 to S7. The description of each table is reported in the first sheet of the file.
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Supplementary weblinks

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