Combinatorial peptide ligand libraries (CPLLs) have been adopted for investigating the proteomes of mango peel and pulp as well their peptidome content (the latter as captured with a C 18 resin). The aim of this study was not only to perform the deepest investigation so far of the mango proteome, but also to assess the potential presence of allergens and of peptides endowed with biological activities. The proteins of peel and pulp have been captured under both native and denaturing extraction techniques. A total of 334 unique protein species have been identified in the peel vs. 2855 in the pulp, via capture with CPLLs at different pH values (2.2 and 7.2).