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.
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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Data repository
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The expanded WormJam chemical list and related MSP libraries, the raw files of LC-MS/MS analyses, and all the tables of features and following elaborations are reported in the linked Zenodo repository.
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Code repository
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All the code written for data elaboration are available in the linked GitHub repository.
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WormJam extended Markdown
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The code to produce the WormJam extended database is available on the linked GitLab repository.
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