Abstract
BackgroundMetabolomics 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.ResultsHere 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-016-0115-8) contains supplementary material, which is available to authorized users.
Highlights
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
We recommend that Galaxy-M workflow files are included within the supplementary information of publications, enabling metabolomics studies to achieve greater reproducibility
The direct infusion mass spectrometry (DIMS) workflow includes a tool named ‘File List Manager’, which takes as input the directory containing the .RAW and .dat files; a .csv file, retrieved from the user history, that contains two columns and an integer value representing the uniform number of replicates for each sample which is stored in the output as a common variable for use in subsequent tools
Summary
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 bring a set of non-targeted DIMS and LC-MS based metabolomics processing and analysis tools into the Galaxy workflow platform.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
