---
title: "PTR-TOF-MS volatolomics datasets description"
author: "Camille Roquencourt, Stanislas Grassin Delyle and Etienne Thevenot"
package: "`r pkg_ver('ptairData')`"
vignette: >
  %\VignetteIndexEntry{PTR-TOF-MS dataset}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
  %\VignetteKeywords{MassSpectrometry, Volatolomics, PTR-TOF-MS}
output:
  BiocStyle::html_document:
    toc: yes
    toc_depth: 4
    toc_float:
      collapsed: false
---


```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# Installation 

```{r, Installation, eval=FALSE }
if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ptairData")
```

# Description

This package contains two volatolomics raw datasets acquired with a Proton-Transfer-Reaction Time-of-Flight mass spectrometer (PTR-TOF-MS; Ionicon Analytik GmbH, Innsbruck, Austria). They are stored in two subfolders:  

- **exhaledAir**: Exhaled air from two healthy individuals, three acquisitions per individual on distinct days [6 files in total], with two expirations per acquisition and Buffered end-tidal (BET) sampling [Herbig et al, 2008](http://stacks.iop.org/1752-7163/2/i=3/a=037008?key=crossref.6c1463e66d0714dce9de2a6cfe05bf66))

- **mycobacteria**: cell culture headspace: two replicates from two species and one control (culture medium only) [6 files]


# Format

The files are in the open Hierarchical Data Format ([HDF5](https://www.hdfgroup.org)). To limit the size of the data and speed up the analysis in demo examples, the raw data are truncated in the m/z dimension within the range $[20.4, 21.6] \cup [50, 150]$ for individuals, and $[20.4, 21.6] \cup [56.4, 90.6]$ for mycobacteria.

# Processing

The ptairMS package (also available on Bioconductor) is devoted to the processing of PTR-TOF-MS data.

# Session info

```{r}
sessionInfo()
```