ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath - CEA - Commissariat à l’énergie atomique et aux énergies alternatives Accéder directement au contenu
Article Dans Une Revue Bioinformatics Année : 2022

ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath

Résumé

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)
Fichier principal
Vignette du fichier
Roquencourt_PtairmsRealTime_2022.pdf (3.15 Mo) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)

Dates et versions

cea-03598858 , version 1 (06-03-2022)

Licence

Paternité - Pas d'utilisation commerciale

Identifiants

Citer

Camille Roquencourt, Stanislas Grassin-Delyle, Etienne A Thévenot. ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath. Bioinformatics, 2022, 38 (7), pp.1930-1937. ⟨10.1093/bioinformatics/btac031⟩. ⟨cea-03598858⟩
131 Consultations
84 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More