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

Rosa Alba Sola Martínez1,2, José María Pastor Hernández1,2, Gema Lozano Terol1,2

  • 1Biotechnology Group, Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain.

Scientific Reports
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This study presents an open-source workflow for analyzing volatile organic compounds (VOCs) in exhaled breath. This method improves data preprocessing for noninvasive disease diagnosis using gas chromatography-mass spectrometry (GC/MS).

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Area of Science:

  • Biomedical Engineering
  • Analytical Chemistry
  • Computational Biology

Background:

  • Noninvasive disease diagnosis is a health priority, with volatile organic compounds (VOCs) showing promise.
  • Current clinical application of VOC analysis is limited by the lack of reproducible protocols, especially in data preprocessing.

Purpose of the Study:

  • To present an open-source workflow for preprocessing exhaled breath sample data obtained via gas chromatography-mass spectrometry (GC/MS).
  • To establish a standardized protocol for collecting exhaled breath samples from infants for GC/MS analysis.

Main Methods:

  • Developed an open-source workflow integrating two approaches to transform raw GC/MS data into a statistically usable matrix.
  • Utilized three free R packages (xcms, cliqueMS, eRah) for data processing and compound matching against a spectral library.
  • Proposed a protocol for collecting exhaled breath samples from infants (<2 years) for GC/MS analysis.

Main Results:

  • The presented workflow effectively preprocesses GC/MS data from exhaled breath samples.
  • The workflow facilitates the identification and matching of volatile organic compounds (VOCs) using spectral libraries.
  • A validated protocol for infant breath sample collection suitable for GC/MS analysis was established.

Conclusions:

  • The developed open-source workflow enhances the reproducibility of VOC biomarker discovery from exhaled breath.
  • This standardized approach is crucial for advancing the clinical utility of GC/MS-based breath analysis for disease diagnosis and monitoring.
  • The protocol for infant sample collection addresses a critical need for pediatric applications.