Liquid chromatography-electrospray ionisation-mass spectrometry (LC-ESI-MS) was applied as an advanced methodology to study the suitability of using α-aminoadipic semialdehyde (AAS) and γ-glutamic semialdehyde (GGS) as protein oxidation markers in meat products. The results obtained were compared to those obtained by using the DNPH-method and fluorescence spectroscopy for the analysis of protein carbonyls. Lipid oxidation was also investigated in order to elucidate the relationship between lipid and protein oxidation measurements. Both semialdehydes were originally detected in a food system which proves that lysine, arginine and proline are degraded as a result of oxidative reactions to yield AAS and GGS in meat products. A lack of consistency was observed between the MS results for AAS and GGS and the values obtained by the DNPH-method and the fluorescence spectroscopy. Unlike the last two methods, AAS and GGS measurements have proved to be unaffected by the composition or the structure of the food matrix providing precise information about the fate of particular amino acids during processing of muscle foods. These semialdehydes, and particularly GGS, could be used as indicators of protein oxidation in meat products like TBARS numbers are commonly used as lipid oxidation markers. In fact, a significant correlation was found between GGS values and TBARS highlighting the timely interaction between lipid and protein oxidation.