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We provide detailed datasets from our analysis of proteins that are identified in human liver, lung, kidney and intestine microsomes by MS-based proteomics. Also included is a set of CYP450 enzymes and microsomal glutathione-S-transferase (MGSTs) activities in human liver microsomes. The data presented in this paper support the research article “Targeted label-free approach for quantification of epoxide hydrolase and glutathione transferases in microsomes” (Song et al., 2015) [1]. We expect that the data will contribute to the study of metabolism enzymes.