The results of an Analysis can be used to identify different metabolites and their concentrations within the Sample analysed. For example, definitive identification of metabolites detected by a GC-MS instrument is performed by matching chromatographic peaks. This can be performed either using external mass spectra libraries or internal libraries obtained by analysing samples of pure chemical standards. In the latter case, the relevant details are recorded and stored as usual: the samples are described using the ChemicalSample component, the experimental protocols and instrument settings are stored using the Admin component, and the analytical results (e.g. the actual peaks produced) are stored using the appropriate classes (depending on the method/instrument used) in the InstrumentalAnalysis component. In addition, each Analysis produced as a characterisation of a given metabolite is used to create a new item in a MetaboliteLibrary. This item corresponds to an instance of MetaboliteLocalDesc, i.e. a local description of a given metabolite. Each local description of a metabolite is further mapped to its global description (class MetaboliteGlobalDesc), where the general information about the metabolite is stored: its identifiers in other resources, its names, molecular formula and weight, SMILES strings, etc.

When performing metabolite identification, using either an external or an internal library, different parameters quantifying the quality of a match are used depending on a specific instrument and software. These attributes are, therefore, recorded in the instrument-specific classes. For example, when a Leco instrument is used for GC-MS analysis, spectrum similarity and reverse matches are used as such attributes in the LecoPeak class. The actual metabolites identified are modelled by the MetaboliteIdentification class, which links the analytical results directly to a local description of a metabolite and indirectly to its global description.