Sea bass represents one of the main fish products in the market. Most of it comes from farming and is bred in different conditons with respect to the wild fish. Differences may thus be expected. In this study, a proteomic profile of farmed and wild sea bass samples was performed, employing a fractionation strategy where peptide samples were first separated by 2D chromatography. The peptides were finally analyzed by shotgun proteomics workflow combined to tandem MS. The chosen fractionation approach was successful allowing to greatly improve the fish muscle protein characterization and detect some interesting differences between wild fish and farmed sea bass. Sixty-nine proteins were overexpressed in farmed fish samples, whereas 182 proteins were underexpressed. Some of these proteins could be related to the breeding conditions and the diet with which fishes were fed, thus providing some interesting results for assessing food quality based on a comprehensive proteomic study.