Quantitative proteomics by 2DE and MALDI MS/MS uncover the effects of organic and conventional cropping methods on vegetable products

► Does organic cropping methods bring more nutritional benefits to consumers than the conventional cropping methods? ► We used 2DE and MALDI MS/MS based proteome analysis to study cabbage (Brassica oleracea) and carrot (Daucus carota) ► We compared proteomes of cabbage and carrot root farmed at one conventional and two organic schemes. ► Proteins of glycolysis, Krebs cycle and amino acid metabolism were overexpressed in organically farmed cabbage. ► Proteins related to detoxification processes were overexpressed in conventionally grown cabbage.