title: Influences of Normalization Method on Biomarker Discovery in Gas Chromatography-Mass Spectrometry-Based Untargeted Metabolomics: What Should Be Considered?
abstract: Data reduction techniques in gas chromatography-mass spectrometry-based untargeted metabolomics has made the following workflow of data analysis more lucid. However, the normalization process still perplexes researchers, and its effects are always ignored. In order to reveal the influences of normalization method, five representative normalization methods (mass spectrometry total useful signal, median, probabilistic quotient normalization, remove unwanted variation-random, and systematic ratio normalization) were compared in three real data sets with different types. First, data reduction techniques were used to refine the original data. Then, quality control samples and relative log abundance plots were utilized to evaluate the unwanted variations and the efficiencies of normalization process. Furthermore, the potential biomarkers which were screened out by the Mann-Whitney U test, receiver operating characteristic curve analysis, random forest, and feature selection algorithm Boruta in different normalized data sets were compared. The results indicated the determination of the normalization method was difficult because the commonly accepted rules were easy to fulfill but different normalization methods had unforeseen influences on both the kind and number of potential biomarkers. Lastly, an integrated strategy for normalization method selection was recommended.
authors.forename: Jiaqing
authors.identifier: 0000-0001-9598-9701
authors.initials: J
authors.lastname: Chen
authors.forename: Pei
authors.initials: P
authors.lastname: Zhang
authors.affiliation: School of Pharmacy, Shihezi University , Shihezi 832002, China.
authors.forename: Mengying
authors.initials: M
authors.lastname: Lv
authors.forename: Huimin
authors.initials: H
authors.lastname: Guo
authors.forename: Yin
authors.identifier: 0000-0001-9678-2630
authors.initials: Y
authors.lastname: Huang
authors.forename: Zunjian
authors.initials: Z
authors.lastname: Zhang
authors.forename: Fengguo
authors.identifier: 0000-0001-9999-0128
authors.initials: F
authors.lastname: Xu
mesh_terms: D019540:Area Under Curve; D015415:Biomarkers / Q000032:analysis* / Q000097:blood; D008401:Gas Chromatography-Mass Spectrometry; D006801:Humans; D007700:Kinetics; D055432:Metabolomics / Q000379:methods*; D012372:ROC Curve
chemical_list: D015415:Biomarkers