Food safety and quality and associated risks are a major concern around the world not only in relation to the relative economic loss but also regarding the potential risk to the health of the consumer. Customer confidence in the safety of the food supply can be hampered by inappropriate food safety measures. A lack of reliable metrics and standards to assess and maintain good control of food quality may affect the economy of the food industry and undermine consumer confidence. It is essential to establish fast and reliable analytical methods that allow a good and rapid analysis of food products throughout the entire food chain. Proteomics can be a powerful tool for addressing this problem, given their excellent quantitative and qualitative deficiencies in protein analysis. This review explains the applications of proteomics in the past few years in food science, with a focus on food of animal origin, with some brief hints about other species. The objective of this review is to highlight the importance of this science as a valuable tool for assessing food quality and safety. Emphasis is also placed on treating food, allergies, and potential contaminants, such as bacteria, fungi, and other pathogens. The application of proteomics to the medical field has led to the study of disease and to the improvement of diagnosis and prognosis. Proteins play an important role in the daily activity of an organism, and the quality and quantity of these proteins depend on various elements, such as life cycle, the environment, stress, stimulus, and gene expression. Hence, these proteins can be used as biomarkers that indicate a specific disease.