Collaborative trial; Environmental exposure; Life course; Non-targeted; Open source tools; Pubchem; Spectra's; Spectral data; Spectral libraries; Work-flows; Environmental Chemistry; Public Health, Environmental and Occupational Health; Management, Monitoring, Policy and Law; General Medicine
Abstract :
[en] The term "exposome" is defined as a comprehensive study of life-course environmental exposures and the associated biological responses. Humans are exposed to many different chemicals, which can pose a major threat to the well-being of humanity. Targeted or non-targeted mass spectrometry techniques are widely used to identify and characterize various environmental stressors when linking exposures to human health. However, identification remains challenging due to the huge chemical space applicable to exposomics, combined with the lack of sufficient relevant entries in spectral libraries. Addressing these challenges requires cheminformatics tools and database resources to share curated open spectral data on chemicals to improve the identification of chemicals in exposomics studies. This article describes efforts to contribute spectra relevant for exposomics to the open mass spectral library MassBank (https://www.massbank.eu) using various open source software efforts, including the R packages RMassBank and Shinyscreen. The experimental spectra were obtained from ten mixtures containing toxicologically relevant chemicals from the US Environmental Protection Agency (EPA) Non-Targeted Analysis Collaborative Trial (ENTACT). Following processing and curation, 5582 spectra from 783 of the 1268 ENTACT compounds were added to MassBank, and through this to other open spectral libraries (e.g., MoNA, GNPS) for community benefit. Additionally, an automated deposition and annotation workflow was developed with PubChem to enable the display of all MassBank mass spectra in PubChem, which is rerun with each MassBank release. The new spectral records have already been used in several studies to increase the confidence in identification in non-target small molecule identification workflows applied to environmental and exposomics research.
Disciplines :
Chemistry
Author, co-author :
ELAPAVALORE, Anjana ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Environmental Cheminformatics
KONDIC, Todor ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Environmental Cheminformatics > Team Emma SCHYMANSKI
SINGH, Randolph ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Environmental Cheminformatics > Team Emma SCHYMANSKI ; IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer), Laboratoire Biogéochimie des Contaminants Organiques, Rue de l'Ile d'Yeu, BP 21105, Nantes Cedex 3, 44311, France
Shoemaker, Benjamin A ; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, 20894, USA
Thiessen, Paul A ; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, 20894, USA
Zhang, Jian ; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, 20894, USA
Bolton, Evan E ; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, 20894, USA
FNR12341006 - Environmental Cheminformatics To Identify Unknown Chemicals And Their Effects, 2018 (01/10/2018-30/09/2023) - Emma Schymanski
Funders :
Fonds National de la Recherche Luxembourg U.S. National Library of Medicine National Institutes of Health
Funding text :
E. L. S., A. E. and T. K. acknowledge funding support from the Luxembourg National Research Fund (FNR) for project A18/BM/12341006. The work of B. A. S., P. A. T., J. Z. and E. E. B. was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health. We would like to thank Adelene Lai for assistance in restoring the stereochemistry information to the MS-ready SMILES (see the Discussion) and acknowledge the other members of the Environmental Cheminformatics (ECI) and PubChem teams, plus the MassBank consortium members and all other contributors to the open science efforts that supported this effort. We gratefully acknowledge the US EPA for providing the mixtures used here as part of the ENTACT trial.
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