The objective of the experiment was to compare the efficiency of drug metabolism in patient-specific hepatocyte organoids (h-HepOrg), periportal liver assembloids (Assmbl) and primary hepatocytes cultured in standard 2D-hepatocyte monolayer culture (Hep2D). The samples were incubated with the pharmaceutical compound verapamil. Following this, verapamil metabolites were measured in the medium and cell extracts by high-resolution mass spectrometry . The quantification of metabolite norverapamil was achieved by utilizing isotopically labelled internal standard 13C3 spiked into samples as described in Yuan etal. The data comprises files in .raw format (ThermoFischerScientific). Files description: 1. type of biological material, donor code and analyzed fraction (supernatant or cell extract) are included in the metadata of each file; 2. each sample was provided in three biological repeats; 3. each biological repeat was measured in four technical replicates.