External Resources

Metabolomics Consortiums, Initiatives, and Societies

• National Institutes of Health (NIH) Common Fund Metabolomics
• COSMOS - COordination of Standards in MetabOlomicS
• MetaboLights
• MetabolomeXchange
• Metabolomics Society
• MetaboNews (newsletter)
• Metabolomics Standards Initiative (MSI)

Metabolomics Databases

Please see our Data section for access to the Metabolomics Workbench Metabolites Database and experimental data from studies conducted by Regional Comprehensive Metabolomics Resource Cores (RCMRCs) and other NIH grantees.

• Biological Magnetic Resonance Data Bank
• Birmingham Metabolite Library collection of 3328 experimental 1D and 2D J-resolved NMR spectra of 208 metabolite standards.
• Biological Magnetic Resonance Data Bank: A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
• Golm Metabolome Database (GMD) Data sets for biologically active metabolites quantified using GC-MS; MS data and text search capabilities.
• Glycan Mass Spectral Database (GMDB) Database of MS spectra data for N- and O-linked glycans and glycolipids glycans along with their partial chemical structures.
• Human Metabolome Database (HMDB) Information about small molecule metabolites found in human body; Metabolite data sets containing MS, GC/MS and NMR information; Search and retrieval capabilities for structure, assay and metabolite data sets. Houses MetabLIMS.
• LIPID MAPS Structure Database (LMSD) The LIPID MAPS Structure Database (LMSD) is comprised of structures and annotations of biologically relevant lipids, and includes representative examples from each category of the LIPID MAPS Lipid Classification System.
• LIPID MAPS Proteome Database (LMPD) Lipid-associated protein sequences with annotations from UniProt, EntrezGene, ENZYME, GO, KEGG and other public resources. Browse or search by species, lipid class association, and/or keywords.
• Madison Metabolomics Consortium Database MS and NMR data sets
• Mass Spectral Library Extensive collection of data sets (EI MS, MS/MS, Replicate spectra, Retention index).
• mzCloud A database of manually curated and recalibrated high-resolution tandem mass spectra of endogenous metabolites, pharmaceuticals and environmental contaminants acquired using CID and HCD techniques
• MetabolomeExpress Private and public repository of un-curated/curated metabolomics data; Interactive tools for data visualization, processing and statistical analysis.
• METLIN: Metabolite and Tandem MS Database Repository of metabolite information and high resolution MS/MS data; Variety of metabolite and MS data search capabilities (MS data search, MS/MS spectral match; Interactive MS spectrum viewer).
• Spectral Database System (SDBS) Repository of spectral database of organic compound; Variety of data sets (MS, NMR, IR, Raman, ESR).

Metabolomics Tools

R Packages for Statistical Analysis

• BATMAN R package for estimating metabolite concentrations from Nuclear Magnetic Resonance spectral data using a specialised MCMC algorithm
• CTSgetRR interface to CTS
• Hierarchical Clustering
• imDEV Microsoft Excel add-in for multivariate analyses in R which include: clustering, PCA, PLS, correlation network mapping
• Linear Discriminant Analysis
• Metabolomics Univariate and Multivariate Analysis
• Principal Components Analysis
• R Package for downloading and parsing mwTab files from the Metabolomics Workbench
• The R Project for Statistical Computing

Other Metabolomics Tools

• 3Omics web tool for visualizing and rapidly integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data.
• ACD/ NMR Processor Academic Edition Free NMR processing software for academic and non-commercial use only.
• CHEMDATA.NIST.GOV Mass spectral libraries and data analysis tools include AMDIS (Automated Mass Spectral Deconvolution and Identification System for GC/MS) and MS Interpreter (for fragmentation analysis).
• Chemical Translation ServiceWeb-based service for metabolite identifier translation between > 200 common biological databases, including: Chemical Name, InChIKey, PubChem, ChemSpider, BioCyc, ChEBI, CAS, HMDB, KEGG and LIPID MAPS.
• Chenomix NMR Suite
• Cytoscape Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
• DeviumWebLocal or web-based data analysis and visualization tool including: dynamic data visualization, data summaries, statistical analysis, clustering, PCA, PLS, O-PLS
• KEGG KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies
• LIPID MAPS toolsMS analysis tools, structure drawing tools, and command line Perl scripts to generate SD files and structure and ontological data for various lipid categories.
• MBrolemetabolite enrichment analysis
• Metaboanalyst Tool suite for metabolomics analysis
• Metacore integrated software suite for functional analysis of microarray, metabolic, SAGE, proteomics, siRNA, microRNA, and screening data.
• MetaMapRLocal or web-based tool for generating biochemical interaction (KEGG), structural similarity (PubChem Substructure Fingerprints), mass spectral similarity and correlation based networks.
• MetaP Serverautomates data analysis for the processing of metabolomics experiments
• MetPA A web-based metabolomics tool for pathway analysis & visualization
• MetExplore MetExplore is a free academic service allowing: Importing/storing/sharing genome scale meta­bolic networks; Map­ping poly­omics data; Path­way enrichment; Visu­al­iz­ing networks; Min­ing net­works based on data and net­work structure; and Com­put­ing fluxes http://nar.oxfordjournals.org/content/38/suppl_2/W132
• MetscapeThe MetScape Plugin for Cytoscape provides a bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data in the context of human metabolism.
• SAS and SAS JMP SAS on the server is for data cleansing, integration, security and access. Applications in JMP extends access to specific SAS software features, procedures and solutions.
• Simca Multivariate statistical analysis (PCA, PLSDA etc.)
• Statistica tools for statistical analysis of data
• TeachingDemosTutorials, case studies and demonstrations of metabolomic data analyses
• TIBCO Spotfire tools for statistical analysis of data
• TransOmics Informatics Platform for bioinformatics, statistical analysis, and reporting of key results.