Multi-omics analyses of the effect of carbon ion beam irradiation on cannabis fructus (Cannabis sativa L.) composition

•Effects of carbon ion beam irradiation on physiological and biochemical pathways of cannabis fructus fruit analyzed using a multi-omics approach.•Carbon ion beam irradiation affects the expression of proteins related to the carbon fixation pathway, fatty acid synthesis pathway, JA synthesis and glutathione metabolism pathway in cannabis fructus.•Carbon ion beam irradiation at a dose of 60 Gy resulted in larger cannabis fructus seeds, higher thousand kernel weight and increased linolenic acid content.