This chapter presents CEU Mass Mediator (CMM), an online tool for aiding researchers in metabolite annotation of mass spectrometry data. It integrates and unifies compounds from different data sources (KEGG, HMDB, LipidMaps, Metlin, an in-house library and MINE) and it incorporates an expert system that applies analytical chemistry knowledge to filter and score the putative annotations retrieved from the data sources. CMM also provides different services for metabolomics, such as a pathway displayer, a quality spectra assessment tool, an MS/MS search and a dedicated service for the annotation of oxidized glycerophosphocholines.