Comparative Evaluation of MS-based Metabolomics Software and Its Application to Preclinical Alzheimer's Disease.
Comparative Evaluation of MS-based Metabolomics Software and Its Application to Preclinical Alzheimer's Disease.
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DOI：
10.1038/s41598-018-27031-x
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发表时间：
2018-06-18
影响因子：
4.6
通讯作者：
Li L
中科院分区：
文献类型：
--
作者：
Hao L;Wang J;Page D;Asthana S;Zetterberg H;Carlsson C;Okonkwo OC;Li L
基于质谱学的代谢组学在过去十年中取得了重大进展，开发了各种用于数据分析的软件包。然而，对不同的代谢组学软件工具进行系统的比较却很少。在本研究中，几个具有代表性的软件包在代谢组学数据分析的整个流程中进行了比较评估，包括数据处理、统计分析、特征选择、代谢物识别、路径分析和分类模型构建。使用少量人脑脊液样本(N = 30)，将基于LC-MS的代谢组学应用于临床前阿尔茨海默病(AD)。所有三个软件包，XCMS Online，Sieve，和Component Discoverer，都提供了一致和可重复的数据处理结果。采用统计检验和支持向量机特征选择相结合的混合方法对关键代谢物进行筛选，实现了对3个软件包中候选生物标志物的互补选择。使用候选生物标志物的机器学习分类生成了高精度和预测性的模型，以将患者分类为临床前AD或对照类别。总体而言，我们的研究展示了对整个数据分析管道中不同的基于MS的代谢组学软件包的系统评估，该软件包应用于临床前AD的候选生物标记物的发现。
Mass spectrometry-based metabolomics has undergone significant progresses in the past decade, with a variety of software packages being developed for data analysis. However, systematic comparison of different metabolomics software tools has rarely been conducted. In this study, several representative software packages were comparatively evaluated throughout the entire pipeline of metabolomics data analysis, including data processing, statistical analysis, feature selection, metabolite identification, pathway analysis, and classification model construction. LC-MS-based metabolomics was applied to preclinical Alzheimer’s disease (AD) using a small cohort of human cerebrospinal fluid (CSF) samples (N = 30). All three software packages, XCMS Online, SIEVE, and Compound Discoverer, provided consistent and reproducible data processing results. A hybrid method combining statistical test and support vector machine feature selection was employed to screen key metabolites, achieving a complementary selection of candidate biomarkers from three software packages. Machine learning classification using candidate biomarkers generated highly accurate and predictive models to classify patients into preclinical AD or control category. Overall, our study demonstrated a systematic evaluation of different MS-based metabolomics software packages for the entire data analysis pipeline which was applied to the candidate biomarker discovery of preclinical AD.
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影响因子：
2.9
作者：
Jiang S;Liang Z;Hao L;Li L
通讯作者：
Li L
DOI：
10.1016/j.jalz.2010.06.001
发表时间：
2011-05
期刊：
Alzheimer's & dementia : the journal of the Alzheimer's Association
影响因子：
--
作者：
Kaddurah-Daouk R;Rozen S;Matson W;Han X;Hulette CM;Burke JR;Doraiswamy PM;Welsh-Bohmer KA
通讯作者：
Welsh-Bohmer KA
影响因子：
7.4
作者：
Melamud E;Vastag L;Rabinowitz JD
通讯作者：
Rabinowitz JD
影响因子：
7.4
作者：
Gowda, Harsha;Ivanisevic, Julijana;Johnson, Caroline H.;Kurczy, Michael E.;Benton, H. Paul;Rinehart, Duane;Thomas Nguyen;Ray, Jayashree;Kuehl, Jennifer;Arevalo, Bernardo;Westenskow, Peter D.;Wang, Junhua;Arkin, Adam P.;Deutschbauer, Adam M.;Patti, Gary J.;Siuzdak, Gary
通讯作者：
Siuzdak, Gary
影响因子：
7.4
作者：
Lommen, Arjen
通讯作者：
Lommen, Arjen