Proteins, peptides and amino acids contribute to physical properties, biological activities and sensory characteristics of foods. Proteins and peptides are widely used in formulated food due their high nutritional value and functional technological properties, such as emulsifying, gelation, foaming, and water binding. The present chapter will discuss the application of mass spectrometry-based techniques for identification and quantification of complex protein and peptide mixtures present in food matrices in order to assess food quality and safety, food authenticity, and functionality. Qualitative and quantitative MS analysis of complex food protein mixtures play a key role in understanding their nature, structure, functional and nutritional properties and impact on human health. Moreover, modern high-resolution mass spectrometry in combination with bioinformatics offers new possibilities for protein characterization, including the post-translational modifications, protein conformations and protein-protein and protein-ligand interactions.