This research focuses on the utilization of proteomics-based approaches to characterize protein-based allergens. Proteomics is one of the most important post-genomic approaches that provide a complete description of a proteome under various pathological and physiological conditions. The study of proteins/peptides comprises a diverse range of approaches aimed at the identification, characterization, and quantification of proteins in simple and complex matrices. We encourage research directed toward the implementation of bioanalytical instrumentation (including liquid chromatography and mass spectrometry) for the characterization and quantification of protein-based allergens in food and biological matrices.