1 Installation

if(!requireNamespace("BiocManager", quietly = TRUE))

2 Introduction

The ptairMS package provides a workflow to process PTR-TOF-MS raw data in the open Hierarchical Data Format 5 (HDF5; .h5 extension), and generate the peak table as an ExpressionSet object for subsequent data analysis with the many methods and packages available in R. Applications include the analysis of exhaled breath, cell culture headspace or ambient air. The package offers several features to check the raw data and tune the few processing parameters. It also enables to include new samples in a study without re-processing all the previous data, providing a convenient management for cohort studies (e.g. duration of the inclusion process, longitudinal studies, etc.).

Proton Transfer Reaction - Mass Spectrometry (PTR-MS) has emerged with excellent sensitivity and specificity for VOC analysis in a wide range of applications, including environment, food quality, and biology (Blake, Monks, and Ellis 2009). In the area of health and care, PTR-MS opens up unique opportunities for real-time analysis at the patient’s bedside.

3 Volatolomics

The characterization of volatile organic compounds (VOCs) emitted by living organisms is of major interest in medicine, food sciences, and ecology. As an example, thousands of VOCs have been identified in the exhaled breath, resulting from normal metabolism or pathological processes (Lacy Costello et al. 2014). The main advantage of breath analysis in medicine is that the sampling is non-invasive (Devillier et al. 2017). Methods based on mass spectrometry (MS) are the reference technologies for VOC analysis because of their sensitivity and large dynamic range.

4 The ptairMS processing workflow