Updated publication reference for PubMed record(s): 28371297, 30451909. The nutritional intervention program “DiOGenes” focuses on how obesity can be prevented and treated from a dietary perspective. We have generated differential plasma proteome profiles in the DiOGenes cohort to identify proteins associated with weight loss and maintenance and explore their relation to body mass index, fat mass, insulin resistance and sensitivity. Relative protein quantification was obtained at baseline and after combined weight loss/maintenance phases using isobaric tagging and MS/MS. 473 subjects were measured at baseline and end of the intervention; 183 proteins were quantified in more than 70% of the plasma samples. The MS-based proteomic analysis of this large cohort of non-diabetic overweight and obese individuals concomitantly identified known and novel proteins associated with weight loss and maintenance. ClinicalTrials.gov Identifier: NCT00390637