With Guide of Spike-in Experiment for Optimizing Workflow of LC-MS data Processing in Metabolomics

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	With Guide of Spike-in Experiment for Optimizing Workflow of LC-MS data Processing in Metabolomics
	Yan, Bing-peng 1,3; Cao, Chun-mei 1,2; Hou, Jin-jun1 ; Bi, Qi-rui 2; Yang, Min 1; Qi, Peng 1; Shi, Xiao-jian 2; Wang, Jian-wei 2; Wu, Wan-ying1 ; Guo, De-an1,2
刊名	NATURAL PRODUCT COMMUNICATIONS
	2017-08
卷号	12 期号:8 页码:1295-1300
关键词	Metabolomics Liquid chromatography-mass spectrometry (LC-MS) Data processing XCMS Spike-in experiment
ISSN号	1934-578X
文献子类	Article; Proceedings Paper
英文摘要	A systematical study was performed to investigate the processing workflow of LC-MS-based metabolomics data by optimizing parameter settings in XCMS software and comparing different preprocessing methods. Here we use a spike-in experiment combining with design of experiment (DoE) approaches for optimizing XCMS software parameters. A trusted index, which was based on accuracy evaluation of the spike-in data, was employed to assess the optimizing process. After optimizing the XCMS setting, the trusted index was improved from 3.67 to 30 and positive rate of spike-in standards also increased from 20% to 100%. Moreover, different data preprocessing methods, such as normalization, different scaling methods were also investigated on spike-in data since they were found to affect the outcome of the data analysis and ions features identification. Accordingly, UN-normalization and Pareto scaling were chosen as appropriate preprocessing methods to deal with LC-MS data through the evaluation of match index (mainly applied multivariate statistics methods). Finally, the optimized workflow was applied to experimental samples that acquired from metabolomics experiment and analyzed randomly with spike-in sample, which indicated a better applicability in formal metabolomics experiment. It is concluded that the proposed data processing workflow could be used as feasible approach for improving the quality of LC-MS-based metabolomics data and ensured the veracity of metabolites identification in data processing procedures to a certain extent.
资助项目	National Natural Science Foundation of China[81403097]
WOS关键词	MASS-SPECTROMETRY DATA ; MOLECULAR PROFILE DATA ; IDENTIFICATION ; METABONOMICS ; STRATEGY ; DESIGN ; MZMINE
WOS研究方向	Pharmacology & Pharmacy ; Food Science & Technology
语种	英语
出版者	NATURAL PRODUCTS INC
WOS记录号	WOS:000408399600039
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/272537]
专题	上海中药现代化研究中心
通讯作者	Wu, Wan-ying; Guo, De-an
作者单位	1.Chinese Acad Sci, Shanghai Inst Mat Med, Shanghai 201203, Peoples R China; 2.Univ Sci & Technol China, Nano Sci & Technol Inst, Suzhou 215123, Peoples R China; 3.China Pharmaceut Univ, Coll Tradit Chinese Med, Nanjing 210009, Jiangsu, Peoples R China
推荐引用方式 GB/T 7714	Yan, Bing-peng,Cao, Chun-mei,Hou, Jin-jun,et al. With Guide of Spike-in Experiment for Optimizing Workflow of LC-MS data Processing in Metabolomics[J]. NATURAL PRODUCT COMMUNICATIONS,2017,12(8):1295-1300.
APA	Yan, Bing-peng.,Cao, Chun-mei.,Hou, Jin-jun.,Bi, Qi-rui.,Yang, Min.,...&Guo, De-an.(2017).With Guide of Spike-in Experiment for Optimizing Workflow of LC-MS data Processing in Metabolomics.NATURAL PRODUCT COMMUNICATIONS,12(8),1295-1300.
MLA	Yan, Bing-peng,et al."With Guide of Spike-in Experiment for Optimizing Workflow of LC-MS data Processing in Metabolomics".NATURAL PRODUCT COMMUNICATIONS 12.8(2017):1295-1300.