Web Server for Peak Detection, Baseline Correction, and Alignment in Two-Dimensional Gas Chromatography Mass Spectrometry-Based Metabolomics Data

Two-dimensional gas chromatography time-of-flight mass spectrometry (GCXGC/TOF-MS) is superior for chromatographic separation and provides great sensitivity for complex biological fluid analysis in metabolomics. However, GCXGC/TOF-MS data processing is currently limited to vendor software and typically requires several preprocessing steps. In this work, we implement a web-based platform, which we call GC(2)MS, to facilitate the application of recent advances in GCXGC/TOF-MS, especially for metabolomics studies. The core processing workflow of GC(2)MS consists of blob/peak detection, baseline correction, and blob alignment. GC(2)MS treats GCXGC/TOF-MS data as pictures and clusters the pixels as blobs according to the brightness of each pixel to generate a blob table. GC(2)MS then aligns the blobs of two GCXGC/TOF-MS data sets according to their distance and similarity. The blob distance and similarity are the Euclidean distance of the first and second retention times of two blobs and the Pearsons correlation coefficient of the two mass spectra, respectively. GC(2)MS also directly corrects the raw data baseline. The analytical performance of GC(2)MS was evaluated using GCXGC/TOF-MS data sets of Angelica sinensis compounds acquired under different experimental conditions and of human plasma samples. The results show that GC(2)MS is an easy-to-use tool for detecting peaks and correcting baselines, and GC(2)MS is able to align GCXGC/TOF-MS data sets acquired under different experimental conditions. GC(2)MS is freely accessible at http://gc2ms.web.cmdm.tw.