Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.
Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.
复制标题
DOI：
10.1186/s13742-016-0115-8
复制
发表时间：
2016
期刊：
影响因子：
9.2
通讯作者：
Viant MR
中科院分区：
文献类型：
--
作者：
Davidson RL;Weber RJ;Liu H;Sharma-Oates A;Viant MR
代谢组学越来越被认为是生物，医学和环境科学的宝贵工具，但落后于其他组学领域的方法成熟度。为了充分发挥其潜力，包括多种组学模式的整合，计算代谢组学工具的可访问性，标准化和再现性必须得到显着改善。在这里，我们介绍了我们在广泛使用的平台Galaxy中的端到端质谱代谢组学工作流程。我们的工作流程名为Galaxy-M，已开发用于直接注入质谱（DIMS）和液相色谱质谱（LC-MS）代谢组学。所介绍的工具范围从原始数据的处理（例如峰值拾取和对齐）到数据清理（例如缺失值插补），再到统计分析的准备（例如标准化和缩放），以及带有相关统计评价的主成分分析（PCA）。我们通过对DIMS和LC-MS数据集的分析展示了使用这些Galaxy工作流程的简便性，并提供PCA评分和相关统计数据，以帮助其他用户确保他们可以准确地重复处理和分析这两个数据集。Galaxy和数据都预装在虚拟机（VM）中，可以从GigaDB存储库下载。此外，源代码、可执行文件和安装说明可从GitHub获得。银河平台使我们能够产生一个易于访问和可重复的计算代谢组学工作流程。社区可以添加更多工具来扩展其功能。我们建议将Galaxy-M工作流程文件包含在出版物的补充信息中，使代谢组学研究能够实现更大的重现性。本文的在线版本（doi：10.1186/s13742-016-0115-8）包含补充材料，可供授权用户使用。
Metabolomics is increasingly recognized as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields. To achieve its full potential, including the integration of multiple omics modalities, the accessibility, standardization and reproducibility of computational metabolomics tools must be improved significantly. Here we present our end-to-end mass spectrometry metabolomics workflow in the widely used platform, Galaxy. Named Galaxy-M, our workflow has been developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics. The range of tools presented spans from processing of raw data, e.g. peak picking and alignment, through data cleansing, e.g. missing value imputation, to preparation for statistical analysis, e.g. normalization and scaling, and principal components analysis (PCA) with associated statistical evaluation. We demonstrate the ease of using these Galaxy workflows via the analysis of DIMS and LC-MS datasets, and provide PCA scores and associated statistics to help other users to ensure that they can accurately repeat the processing and analysis of these two datasets. Galaxy and data are all provided pre-installed in a virtual machine (VM) that can be downloaded from the GigaDB repository. Additionally, source code, executables and installation instructions are available from GitHub. The Galaxy platform has enabled us to produce an easily accessible and reproducible computational metabolomics workflow. More tools could be added by the community to expand its functionality. We recommend that Galaxy-M workflow files are included within the supplementary information of publications, enabling metabolomics studies to achieve greater reproducibility. The online version of this article (doi:10.1186/s13742-016-0115-8) contains supplementary material, which is available to authorized users.