دورية أكاديمية
Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures.
| العنوان: | Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures. |
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| المؤلفون: | Elapavalore A; Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg. anjana.elapavalore@uni.lu., Kondić T; Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg. anjana.elapavalore@uni.lu., Singh RR; Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg. anjana.elapavalore@uni.lu.; 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 BA; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, 20894, USA., Thiessen PA; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, 20894, USA., Zhang J; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, 20894, USA., Bolton EE; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, 20894, USA., Schymanski EL; Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg. anjana.elapavalore@uni.lu. |
| المصدر: | Environmental science. Processes & impacts [Environ Sci Process Impacts] 2023 Nov 15; Vol. 25 (11), pp. 1788-1801. Date of Electronic Publication: 2023 Nov 15. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Royal Society of Chemistry Country of Publication: England NLM ID: 101601576 Publication Model: Electronic Cited Medium: Internet ISSN: 2050-7895 (Electronic) Linking ISSN: 20507887 NLM ISO Abbreviation: Environ Sci Process Impacts Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Cambridge : Royal Society of Chemistry |
| مواضيع طبية MeSH: | Environmental Exposure*/analysis , Software*, Humans ; Mass Spectrometry/methods ; Databases, Factual |
| مستخلص: | 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. |
| التعليقات: | Comment in: Environ Sci Process Impacts. 2023 Nov 15;25(11):1741-1742. (PMID: 37934503) |
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| تواريخ الأحداث: | Date Created: 20230711 Date Completed: 20231201 Latest Revision: 20231201 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC10648001 |
| DOI: | 10.1039/d3em00181d |
| PMID: | 37431591 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 2050-7895 |
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| DOI: | 10.1039/d3em00181d |