<jats:title>Abstract</jats:title><jats:p>Application of mass spectrometry enables the detection of metabolic differences between groups of related organisms. Differences in the metabolic fingerprints of wild-type <jats:italic>Solanum lycopersicum</jats:italic> and three monogenic mutants, <jats:italic>ripening inhibitor</jats:italic> (<jats:italic>rin</jats:italic>), <jats:italic>non-ripening</jats:italic> (<jats:italic>nor</jats:italic>) and <jats:italic>Colourless non-ripening</jats:italic> (<jats:italic>Cnr</jats:italic>), of tomato are captured with regard to ripening behaviour. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a time series of the ripening behaviour at discrete intervals with a focus on changes post-anthesis. Internal standards and quality controls were used to ensure system stability. The raw data of the samples and reference compounds including study protocols have been deposited in the open metabolomics database MetaboLights <jats:italic>via</jats:italic> the metadata annotation tool Isatab to enable efficient re-use of the datasets, such as in metabolomics cross-study comparisons or data fusion exercises.