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Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures
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 a...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society of Chemistry
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10648001/ https://www.ncbi.nlm.nih.gov/pubmed/37431591 http://dx.doi.org/10.1039/d3em00181d |
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author | Elapavalore, Anjana Kondić, Todor Singh, Randolph R. Shoemaker, Benjamin A. Thiessen, Paul A. Zhang, Jian Bolton, Evan E. Schymanski, Emma L. |
author_facet | Elapavalore, Anjana Kondić, Todor Singh, Randolph R. Shoemaker, Benjamin A. Thiessen, Paul A. Zhang, Jian Bolton, Evan E. Schymanski, Emma L. |
author_sort | Elapavalore, Anjana |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10648001 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | The Royal Society of Chemistry |
record_format | MEDLINE/PubMed |
spelling | pubmed-106480012023-07-10 Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures Elapavalore, Anjana Kondić, Todor Singh, Randolph R. Shoemaker, Benjamin A. Thiessen, Paul A. Zhang, Jian Bolton, Evan E. Schymanski, Emma L. Environ Sci Process Impacts Chemistry 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. The Royal Society of Chemistry 2023-07-10 /pmc/articles/PMC10648001/ /pubmed/37431591 http://dx.doi.org/10.1039/d3em00181d Text en This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by/3.0/ |
spellingShingle | Chemistry Elapavalore, Anjana Kondić, Todor Singh, Randolph R. Shoemaker, Benjamin A. Thiessen, Paul A. Zhang, Jian Bolton, Evan E. Schymanski, Emma L. Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures |
title | Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures |
title_full | Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures |
title_fullStr | Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures |
title_full_unstemmed | Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures |
title_short | Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures |
title_sort | adding open spectral data to massbank and pubchem using open source tools to support non-targeted exposomics of mixtures |
topic | Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10648001/ https://www.ncbi.nlm.nih.gov/pubmed/37431591 http://dx.doi.org/10.1039/d3em00181d |
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