| Title: | ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath |
| Author(s): | Roquencourt C; Grassin-Delyle S; Thevenot EA; |
| Address: | "Departement Metrologie Instrumentation & Information (DM2I), CEA, LIST, Laboratoire Sciences des Donnees et de la Decision, F-91191 Gif-Sur-Yvette, France. Departement des maladies des voies respiratoires, Hopital Foch, Exhalomics, Suresnes 92150, France. Departement de Biotechnologie de la Sante, Universite Paris-Saclay, UVSQ, INSERM, Infection et inflammation, Montigny le Bretonneux 78180, France. FHU SEPSIS (Saclay and Paris Seine Nord Endeavour to PerSonalize Interventions for Sepsis), Garches 92380, France. Departement Medicaments et Technologies pour la Sante (MTS), Universite Paris-Saclay, CEA, INRAE, MetaboHUB, F-91191 Gif sur Yvette, France" |
| DOI: | 10.1093/bioinformatics/btac031 |
| ISSN/ISBN: | 1367-4811 (Electronic) 1367-4803 (Print) 1367-4803 (Linking) |
| Abstract: | "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" |
| Keywords: | Humans Protons Breath Tests/methods *Time Perception Reaction Time Mass Spectrometry/methods *Volatile Organic Compounds/analysis Biomarkers/analysis; |
| Notes: | "MedlineRoquencourt, Camille Grassin-Delyle, Stanislas Thevenot, Etienne A eng Research Support, Non-U.S. Gov't England 2022/01/20 Bioinformatics. 2022 Mar 28; 38(7):1930-1937. doi: 10.1093/bioinformatics/btac031" |
