QPMASS: A parallel peak alignment and quantification software for the analysis of large-scale gas chromatography-mass spectrometry (GC-MS)-based metabolomics datasets

doi:10.1016/j.chroma.2020.460999

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	QPMASS: A parallel peak alignment and quantification software for the analysis of large-scale gas chromatography-mass spectrometry (GC-MS)-based metabolomics datasets
	Duan, Lixin 5; Ma, Aimin 1,2; Meng, Xianbin ; Shen, Guo-an ; Qi, Xiaoquan 2
刊名	JOURNAL OF CHROMATOGRAPHY A
	2020
卷号	1620
关键词	QPMASS GC-MS Metabolomics Data analysis Parallel computing
ISSN号	0021-9673
DOI	10.1016/j.chroma.2020.460999
文献子类	Article
英文摘要	Gas chromatography-mass spectrometry (GC-MS) is a robust analytical platform for analysis of small molecules. Recently, it is widely used for large-scale metabolomics studies, in which hundreds or even thousands of samples are analyzed simultaneously, producing a very large and complex GC-MS datasets. A number of software are currently available for processing GC-MS data, but it is too compute-intensive for them to efficiently and accurately align chromatographic peaks from thousands of samples. Here, we report a newly developed software, QPMASS, for analysis of large-scale GC-MS data. The parallel computing with an advanced dynamic programming approach is implemented in QPMASS to align peaks from multiple samples based on retention time and mass spectra, enabling fast processing large-scale datasets. Furthermore, the missing value filtering and backfilling are introduced into the program, greatly reducing false positive and false negative errors to be less than 5%. We demonstrated that it took only 8 h to align and quantify a GC-TOF-MS dataset from 300 rice leaves samples, and 17 h to process a GC-qMS dataset from 1000 rice seed samples by using a personal computer (3.70 GHz CPU, 16 GB of memory and > 100 GB hard disk). QPMASS is written in C++ programming language, and is able to run under Windows operation system with a user-friendly interface. (C) 2020 Elsevier B.V. All rights reserved.
学科主题	Biochemical Research Methods ; Chemistry, Analytical
电子版国际标准刊号	1873-3778
出版地	AMSTERDAM
WOS关键词	GC/TOF-MS DATA ; DECONVOLUTION ; TOOL ; IDENTIFICATION ; METABOLITES ; EXTRACTION ; RNA
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry
语种	英语
出版者	ELSEVIER
WOS记录号	WOS:000530686600023
资助机构	National Key Research and Development Program of China [2016YFD0100904] ; Strategic Priority Research Program of the Chinese Academy of SciencesChinese Academy of Sciences [XDB27010202] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31530050, 81874333, 31570306] ; Science and Technology Program of Guangzhou, China [2018-1002-SF-0437]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/21769]
专题	中科院植物分子生理学重点实验室
作者单位	1.Guangzhou Univ Chinese Med, Int Inst Translat Chinese Med, Guangzhou 510006, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Innovat Acad Seed Design, Beijing 100049, Peoples R China 4.Chinese Acad Med Sci, Peking Union Med Coll, Inst Med Plant Dev, Beijing 100193, Peoples R China 5.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Duan, Lixin,Ma, Aimin,Meng, Xianbin,et al. QPMASS: A parallel peak alignment and quantification software for the analysis of large-scale gas chromatography-mass spectrometry (GC-MS)-based metabolomics datasets[J]. JOURNAL OF CHROMATOGRAPHY A,2020,1620.
APA	Duan, Lixin,Ma, Aimin,Meng, Xianbin,Shen, Guo-an,&Qi, Xiaoquan.(2020).QPMASS: A parallel peak alignment and quantification software for the analysis of large-scale gas chromatography-mass spectrometry (GC-MS)-based metabolomics datasets.JOURNAL OF CHROMATOGRAPHY A,1620.
MLA	Duan, Lixin,et al."QPMASS: A parallel peak alignment and quantification software for the analysis of large-scale gas chromatography-mass spectrometry (GC-MS)-based metabolomics datasets".JOURNAL OF CHROMATOGRAPHY A 1620(2020).