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Mitchell JM, Chi Y, Thapa M, Pang Z, Xia J, Li S. Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580048. [PMID: 38405981 PMCID: PMC10888883 DOI: 10.1101/2024.02.13.580048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
To standardize metabolomics data analysis and facilitate future computational developments, it is essential is have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a full-featured Python-centric pipeline. We demonstrate the performance of the pipeline, and the details in annotation and quality control using large-scale LC-MS metabolomics and lipidomics data and LC-MS/MS data. Multiple previously published datasets are also reanalyzed to showcase its utility in biological data analysis. This pipeline allows users to streamline data processing, quality control, annotation, and standardization in an efficient and transparent manner. This work fills a major gap in the Python ecosystem for computational metabolomics.
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Affiliation(s)
- Joshua M. Mitchell
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Yuanye Chi
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Maheshwor Thapa
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Zhiqiang Pang
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
- University of Connecticut School of Medicine, Farmington, CT 06032, USA
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Pelkonen O, Abass K, Parra Morte JM, Panzarea M, Testai E, Rudaz S, Louisse J, Gundert-Remy U, Wolterink G, Jean-Lou CM D, Coecke S, Bernasconi C. Metabolites in the regulatory risk assessment of pesticides in the EU. FRONTIERS IN TOXICOLOGY 2023; 5:1304885. [PMID: 38188093 PMCID: PMC10770266 DOI: 10.3389/ftox.2023.1304885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
A large majority of chemicals is converted into metabolites through xenobiotic-metabolising enzymes. Metabolites may present a spectrum of characteristics varying from similar to vastly different compared with the parent compound in terms of both toxicokinetics and toxicodynamics. In the pesticide arena, the role of metabolism and metabolites is increasingly recognised as a significant factor particularly for the design and interpretation of mammalian toxicological studies and in the toxicity assessment of pesticide/metabolite-associated issues for hazard characterization and risk assessment purposes, including the role of metabolites as parts in various residues in ecotoxicological adversities. This is of particular relevance to pesticide metabolites that are unique to humans in comparison with metabolites found in in vitro or in vivo animal studies, but also to disproportionate metabolites (quantitative differences) between humans and mammalian species. Presence of unique or disproportionate metabolites may underlie potential toxicological concerns. This review aims to present the current state-of-the-art of comparative metabolism and metabolites in pesticide research for hazard and risk assessment, including One Health perspectives, and future research needs based on the experiences gained at the European Food Safety Authority.
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Affiliation(s)
- Olavi Pelkonen
- Research Unit of Biomedicine, Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Khaled Abass
- Department of Environmental Health Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research (SIMR), University of Sharjah, Sharjah, United Arab Emirates
- Research Unit of Biomedicine and Internal Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | | | | | - Emanuela Testai
- Mechanisms, Biomarkers and Models Unit, Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, CMU, Geneva, Switzerland
| | - Jochem Louisse
- EFSA, European Food Safety Authority, Parma, Italy
- Wageningen Food Safety Research (WFSR), Wageningen, Netherlands
| | - Ursula Gundert-Remy
- Institute of Clinical Pharmacology and Toxicology, Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gerrit Wolterink
- Centre for Prevention, Lifestyle and Health, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | - Sandra Coecke
- European Commission, Joint Research Centre (JRC), Ispra, Italy
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