Publication: Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources
Authors
Pastor Hernández, José María ; Lozano-Terol, Gema ; García-Marcos Álvarez, Luis Vicente ; Cánovas Díaz, Manuel ; Diego Puente, Teresa de ; Gallego Jara, Julia ; Sola Martínez, Rosa Alba
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Publisher
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DOI
10.1038/s41598-020-79014-6
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info:eu-repo/semantics/article
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.
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Citation
Scientific Reports | (2020) 10:22008
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