ptairMS

ptairMS implements a suite of methods to preprocess data from PTR-TOF-MS instruments in HDF5 format and generates the sample by features table of peak intensities with sample and feature metadata as an ExpressionSet object for subsequent statistical analysis.

Key Features:

• Data Preprocessing: Performs calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation, and feature annotation on PTR-TOF-MS data.
• Output Generation: Produces a sample by features table of peak intensities with sample and feature metadata as a single ExpressionSet object.
• Cohort Management: Supports progressive analysis of data across cohorts.
• Quality Control: Includes quality control functionality for processed data.
• Visualization: Provides visualization tools for data exploration.

Scientific Applications:

• Exhaled Air Analysis: Applicable to exhaled air studies as described in vignettes and examples.
• Cell Culture Headspace Analysis: Applicable to cell culture in headspace studies as described in vignettes and examples.
• Biomarker Discovery: Used to identify four potential biomarkers of infection in a study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS).

Methodology:

The computational steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation, and feature annotation. Input data are in HDF5 format from PTR-TOF-MS instruments.