Structural modifications induced by industrial treatments on milk proteins have been investigated using a new analytical protocol based on mass spectrometric procedures (electrospray and matrix assisted laser desorption ionization mass spectrometry) providing a direct correlation between the severity of the treatment and the damages observed. The application of this procedure to the analysis of whey proteins from milk samples submitted to different thermal processes confirmed that under these conditions protein modification is essentially due to the nonenzymatic glycation of amino groups by lactose (Maillard reaction). A detailed structural investigation of the modification sites, carried out by the mass mapping strategy, revealed the occurrence of preferentially lactosylated sites in both alpha-lactalbumin and beta-lactoglobulin.