Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources

Abstract The noninvasive diagnosis and monitoring of high prevalence diseases such as cardiovascular diseases, cancers and chronic respiratory diseases are currently priority objectives in the area of health. In this regard, the analysis of volatile organic compounds (VOCs) has been identified as a...

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Autores principales:	Rosa Alba Sola Martínez, José María Pastor Hernández, Gema Lozano Terol, Julia Gallego-Jara, Luis García-Marcos, Manuel Cánovas Díaz, Teresa de Diego Puente
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0c1818f732ec47778a753f50b5d846c8
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spelling	oai:doaj.org-article:0c1818f732ec47778a753f50b5d846c82021-12-02T13:34:10ZData preprocessing workflow for exhaled breath analysis by GC/MS using open sources10.1038/s41598-020-79014-62045-2322https://doaj.org/article/0c1818f732ec47778a753f50b5d846c82020-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-79014-6https://doaj.org/toc/2045-2322Abstract The noninvasive diagnosis and monitoring of high prevalence diseases such as cardiovascular diseases, cancers and chronic respiratory diseases are currently priority objectives in the area of health. In this regard, the analysis of volatile organic compounds (VOCs) has been identified as a potential noninvasive tool for the diagnosis and surveillance of several diseases. Despite the advantages of this strategy, it is not yet a routine clinical tool. The lack of reproducible protocols for each step of the biomarker discovery phase is an obstacle of the current state. Specifically, this issue is present at the data preprocessing step. Thus, an open source workflow for preprocessing the data obtained by the analysis of exhaled breath samples using gas chromatography coupled with single quadrupole mass spectrometry (GC/MS) is presented in this paper. This workflow is based on the connection of two approaches to transform raw data into a useful matrix for statistical analysis. Moreover, this workflow includes matching compounds from breath samples with a spectral library. Three free packages (xcms, cliqueMS and eRah) written in the language R are used for this purpose. Furthermore, this paper presents a suitable protocol for exhaled breath sample collection from infants under 2 years of age for GC/MS.Rosa Alba Sola MartínezJosé María Pastor HernándezGema Lozano TerolJulia Gallego-JaraLuis García-MarcosManuel Cánovas DíazTeresa de Diego PuenteNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-11 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rosa Alba Sola Martínez José María Pastor Hernández Gema Lozano Terol Julia Gallego-Jara Luis García-Marcos Manuel Cánovas Díaz Teresa de Diego Puente Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources
description	Abstract The noninvasive diagnosis and monitoring of high prevalence diseases such as cardiovascular diseases, cancers and chronic respiratory diseases are currently priority objectives in the area of health. In this regard, the analysis of volatile organic compounds (VOCs) has been identified as a potential noninvasive tool for the diagnosis and surveillance of several diseases. Despite the advantages of this strategy, it is not yet a routine clinical tool. The lack of reproducible protocols for each step of the biomarker discovery phase is an obstacle of the current state. Specifically, this issue is present at the data preprocessing step. Thus, an open source workflow for preprocessing the data obtained by the analysis of exhaled breath samples using gas chromatography coupled with single quadrupole mass spectrometry (GC/MS) is presented in this paper. This workflow is based on the connection of two approaches to transform raw data into a useful matrix for statistical analysis. Moreover, this workflow includes matching compounds from breath samples with a spectral library. Three free packages (xcms, cliqueMS and eRah) written in the language R are used for this purpose. Furthermore, this paper presents a suitable protocol for exhaled breath sample collection from infants under 2 years of age for GC/MS.
format	article
author	Rosa Alba Sola Martínez José María Pastor Hernández Gema Lozano Terol Julia Gallego-Jara Luis García-Marcos Manuel Cánovas Díaz Teresa de Diego Puente
author_facet	Rosa Alba Sola Martínez José María Pastor Hernández Gema Lozano Terol Julia Gallego-Jara Luis García-Marcos Manuel Cánovas Díaz Teresa de Diego Puente
author_sort	Rosa Alba Sola Martínez
title	Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources
title_short	Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources
title_full	Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources
title_fullStr	Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources
title_full_unstemmed	Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources
title_sort	data preprocessing workflow for exhaled breath analysis by gc/ms using open sources
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/0c1818f732ec47778a753f50b5d846c8
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Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources

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