For more than 15 years, our team based at CEA Saclay in the LI-MS laboratory (Laboratory of innovations in mass spectrometry for health), member of the MetaboHUB infrastructure in metabolomics and fluxomics, has been developing innovative computational methods and software libraries applied to metabolomic data science for health. Our know-how and the digital ecosystem we have built cover all steps from signal processing of mass spectrometry data, machine learning, feature selection, data integration, cheminformatics and up to reproducible workflow management.