Systems biology R2DGC: Threshold-free peak alignment and identifica- tion for 2D gas chromatography mass spectrometry in R

Summary: Comprehensive two dimensional gas chromatography-mass spectrometry is a powerful method for analyzing complex mixtures of volatile compounds. This method produces a large amount of raw data that requires downstream processing to align signals of interest (peaks) across multiple samples and match peak characteristics to reference standard libraries prior to downstream statistical analysis. To address the paucity of applications addressing this need, we have developed an R package that implements retention time and mass spectra similarity threshold-free alignments, seamlessly integrates retention time standards for universally reproducible alignments, performs common ion filtering, and provides compatibility with multiple peak quantification methods. We demonstrate the package’s utility on a controlled mix of metabolite standards separated under variable chromatography conditions and data generated from cell lines. Availability and documentation: R2DGC can be downloaded at https://github.com/rramaker/R2DGC or installed via the Comprehensive R Archive Network (CRAN). Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.