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 (GC×GC/TOF-MS) is superior for chromatographic separation and provides great sensitivity for complex biological fluid analysis in metabolomics. However, GC×GC/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 GC2MS, to facilitate the application of recent advances in GC×GC/TOF-MS, especially for metabolomics studies. The core processing workflow of GC2MS consists of blob/peak detection, baseline correction, and blob alignment. GC2MS treats GC×GC/TOF-MS data as pictures and clusters the pixels as blobs according to the brightness of each pixel to generate a blob table. GC2MS then aligns the blobs of two GC×GC/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 Pearson's correlation coefficient of the two mass spectra, respectively. GC2MS also directly corrects the raw data baseline. The analytical performance of GC2MS was evaluated using GC×GC/TOF-MS data sets of Angelica sinensis compounds acquired under different experimental conditions and of human plasma samples. The results show that GC2MS is an easy-to-use tool for detecting peaks and correcting baselines, and GC2MS is able to align GC×GC/TOF-MS data sets acquired under different experimental conditions. GC2MS is freely accessible at http://gc2ms.web.cmdm.tw .
Department of Computer Science and Information Engineering, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.|The Metabolomics Core Laboratory, Center of Genomic Medicine, National Taiwan University , No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.
Tze-Feng
TF
Tian
Department of Computer Science and Information Engineering, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.|The Metabolomics Core Laboratory, Center of Genomic Medicine, National Taiwan University , No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.
San-Yuan
SY
Wang
The Metabolomics Core Laboratory, Center of Genomic Medicine, National Taiwan University , No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.|Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
Tien-Chueh
TC
Kuo
Department of Computer Science and Information Engineering, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.|The Metabolomics Core Laboratory, Center of Genomic Medicine, National Taiwan University , No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.
Cheng-En
CE
Tan
The Metabolomics Core Laboratory, Center of Genomic Medicine, National Taiwan University , No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.|School of Pharmacy, College of Medicine, National Taiwan University , No. 33, Linsen S. Road, Taipei 100, Taiwan.
Guan-Yuan
GY
Chen
The Metabolomics Core Laboratory, Center of Genomic Medicine, National Taiwan University , No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.|School of Pharmacy, College of Medicine, National Taiwan University , No. 33, Linsen S. Road, Taipei 100, Taiwan.|Department of Pharmacy, National Taiwan University Hospital, National Taiwan University , No. 1, Changde Street, Taipei 10048, Taiwan.
Ching-Hua
CH
Kuo
Institute of Occupational Medicine and Industrial Hygiene, National Taiwan University , No. 17, Xuzhou Road, Taipei 100, Taiwan.
Chi-Hsin Sally
CS
Chen
Institute of Occupational Medicine and Industrial Hygiene, National Taiwan University , No. 17, Xuzhou Road, Taipei 100, Taiwan.
Chang-Chuan
CC
Chan
Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
Olivia A
OA
Lin
Department of Computer Science and Information Engineering, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.|The Metabolomics Core Laboratory, Center of Genomic Medicine, National Taiwan University , No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.|School of Pharmacy, College of Medicine, National Taiwan University , No. 33, Linsen S. Road, Taipei 100, Taiwan.|Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
Y Jane
YJ
Tseng
D000465:Algorithms; D029971:Angelica sinensis / Q000737:chemistry / Q000378:metabolism; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods*; D006801:Humans; D020407:Internet; D055432:Metabolomics / Q000379:methods*; D010949:Plasma / Q000737:chemistry / Q000378:metabolism; D012984:Software; D057188:Workflow