We present a theoretical study of the size and structure selective absorption properties of cationic silver cluster-tryptophan Trp-Ag(n)(+) (n = 2-5,9) hybrid systems supported by photofragmentation experiments. Our time-dependent density functional theory calculations provide insight into the nature of excitations in interacting nanoparticle-biomolecule subunits and allow to determine characteristic spectral features as fingerprints of two different classes of structures: charge solvated and zwitterionic. Moreover, different types of charge transfer transitions have been identified. Charge transfer from pi system of tryptophan to silver cluster occurs for charge solvated structures while charge transfer from silver to the NH(3) (+) group takes place for zwitterionic structures. This has been confirmed by experimentally measured photofragmentation channels and molecular dynamics simulations. Our findings provide fundamental insight into the structure- and size-dependent mechanism responsible for the enhanced absorption and emission in nanoparticle-biomolecular hybrid systems.