ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath Article Swipe
Camille Roquencourt
,
Stanislas Grassin‐Delyle
,
Etienne Thévenot
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btac031
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btac031
Motivation Analysis of volatile organic compounds (VOCs) in exhaled breath by proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) is of increasing interest for real-time, non-invasive diagnosis, phenotyping and therapeutic drug monitoring in the clinics. However, there is currently a lack of methods and software tools for the processing of PTR-TOF-MS data from cohorts and suited for biomarker discovery studies. Results We developed a comprehensive suite of algorithms that process raw data from patient acquisitions and generate the table of feature intensities. Notably, we included an innovative two-dimensional peak deconvolution model based on penalized splines signal regression for accurate estimation of the temporal profile and feature quantification, as well as a method to specifically select the VOCs from exhaled breath. The workflow was implemented as the ptairMS software, which contains a graphical interface to facilitate cohort management and data analysis. The approach was validated on both simulated and experimental datasets, and we showed that the sensitivity and specificity of the VOC detection reached 99% and 98.4%, respectively, and that the error of quantification was below 8.1% for concentrations down to 19 ppb. Availability and implementation The ptairMS software is publicly available as an R package on Bioconductor (doi: 10.18129/B9.bioc.ptairMS), as well as its companion experiment package ptairData (doi: 10.18129/B9.bioc.ptairData). Supplementary information Supplementary data are available at Bioinformatics online.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bioinformatics/btac031
- https://academic.oup.com/bioinformatics/article-pdf/38/7/1930/43113417/btac031.pdf
- OA Status
- bronze
- Cited By
- 19
- References
- 59
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4206546952
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4206546952Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bioinformatics/btac031Digital Object Identifier
- Title
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ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breathWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-01-16Full publication date if available
- Authors
-
Camille Roquencourt, Stanislas Grassin‐Delyle, Etienne ThévenotList of authors in order
- Landing page
-
https://doi.org/10.1093/bioinformatics/btac031Publisher landing page
- PDF URL
-
https://academic.oup.com/bioinformatics/article-pdf/38/7/1930/43113417/btac031.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
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bronzeOpen access status per OpenAlex
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https://academic.oup.com/bioinformatics/article-pdf/38/7/1930/43113417/btac031.pdfDirect OA link when available
- Concepts
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Computer science, Data mining, Bioconductor, Software, Biomarker discovery, Breath gas analysis, Pattern recognition (psychology), Artificial intelligence, Chemistry, Chromatography, Proteomics, Gene, Biochemistry, Programming languageTop concepts (fields/topics) attached by OpenAlex
- Cited by
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19Total citation count in OpenAlex
- Citations by year (recent)
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2025: 6, 2024: 4, 2023: 8, 2022: 1Per-year citation counts (last 5 years)
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59Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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