title: Global peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using point matching algorithms.
abstract: Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC[Formula: see text][Formula: see text][Formula: see text]GC-MS) has been used to analyze multiple samples in a metabolomics study. However, due to some uncontrollable experimental conditions, such as the differences in temperature or pressure, matrix effects on samples and stationary phase degradation, there is always a shift of retention times in the two GC columns between samples. In order to correct the retention time shifts in GC[Formula: see text][Formula: see text][Formula: see text]GC-MS, the peak alignment is a crucial data analysis step to recognize the peaks generated by the same metabolite in different samples. Two approaches have been developed for GC[Formula: see text][Formula: see text][Formula: see text]GC-MS data alignment: profile alignment and peak matching alignment. However, these existing alignment methods are all based on a local alignment, resulting that a peak may not be correctly aligned in a dense chromatographic region where many peaks are present in a small region. False alignment will result in false discovery in the downstream statistical analysis. We, therefore, develop a global comparison-based peak alignment method using point matching algorithm (PMA-PA) for both homogeneous and heterogeneous data. The developed algorithm PMA-PA first extracts feature points (peaks) in the chromatography and then searches globally the matching peaks in the consecutive chromatography by adopting the projection of rigid and nonrigid transformation. PMA-PA is further applied to two real experimental data sets, showing that PMA-PA is a promising peak alignment algorithm for both homogenous and heterogeneous data in terms of [Formula: see text]1 score, although it uses only peak location information.
authors.affiliation: * Department of Mathematics, Wayne State University, Detroit, MI, 48201, USA.
authors.forename: Beichuan
authors.initials: B
authors.lastname: Deng
authors.affiliation: † Biostatistics Core, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA.|‡ Department of Oncology, School of Medicine, Wayne State University Detroit, MI 48201, USA.
authors.forename: Seongho
authors.initials: S
authors.lastname: Kim
authors.affiliation: * Department of Mathematics, Wayne State University, Detroit, MI, 48201, USA.
authors.forename: Hengguang
authors.initials: H
authors.lastname: Li
authors.affiliation: ‡ Department of Oncology, School of Medicine, Wayne State University Detroit, MI 48201, USA.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Heath
authors.affiliation: § Department of Chemistry, University of Louisville, Louisville, KY 46209, USA.
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods*; D012815:Signal Processing, Computer-Assisted; D013696:Temperature
keywords: GC-MS; metabolomics; peak alignment; point matching algorithm