gcxgclab: An R Package for Two-Dimensional Gas Chromatography Preprocessing and Analysis

Comprehensive two-dimensional gas chromatography (GC×GC) is an established technique capable of chromatographically separating thousands of analytes in complex matrices. When coupled with highly sensitive detectors such as a high-resolution mass spectrometer, these instruments produce large multidimensional data sets. A prevailing challenge for GC×GC users is efficient data handling and analysis. Although commercial software packages exist for GC×GC data analysis, these platforms are typically optimized for low-throughput qualitative data interpretation utilizing desktop computer systems. Additionally, commercial GC×GC data processing packages offer little flexibility to explore custom or novel data processing concepts. In this work, an open-source R package, called "gcxgclab", was developed as an alternative data processing package for GC×GC users and offers data preprocessing and analysis functions including baseline correction, smoothing, phase shift, peak detection, peak alignment, extracted ion chromatogram, mass spectra extraction, mass defect analysis, and targeted and nontargeted analysis. This package was designed to be customizable and allows for batch data processing on desktops or high-performance computing systems to increase the throughput. gcxgclab is available for free on the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/gcxgclab/index.html.