A recent Nucleic Acids Research (NAR) paper features Metaboligths: the first general-purpose, open access repository for metabolomics studies, storing the studies raw experimental data and associated metadata. You can find the paper here. Metabolights is powered by the the open source ISA metadata framework, and thus is part of the ISA commons, and it is deployed at the European Bioinformatics Institute (EBI).
Some of the characteristics of the database are: it is cross-species and cross-techniques, it covers metabolite structures and their reference spectra, their biological roles, locations, concentrations, and raw data from metabolic experiments.
The paper describes the database content and technical architecture, the functionalities for searching and browsing the data, how to download data and get programmatic access to the database, and the data submission process, among other things.