Proteins are major biological targets for oxidative damage within cells owing to their high abundance and rapid rates of reaction with radicals and excited-state species, including singlet oxygen. Reaction of Tyr, Trp, and His residues, both free and on proteins, with singlet oxygen generates peroxides in high yield. Peroxides have also been detected on proteins within intact cells on exposure to visible light in the presence of a photosensitizer. The structures of some of these materials have been elucidated for free amino acids, but less is known about peptide- and protein-bound species. In this study we have characterized Trp-derived peroxides, radicals, and breakdown products generated on free Trp and Trp residues in peptides and proteins, using LC/MS/MS. With free Trp, seven major photoproducts were characterized, including two isomeric hydroperoxides, two alcohols, two diols, and N-formylkynurenine, consistent with singlet oxygen-mediated reactions. The hydroperoxides decompose rapidly at elevated temperatures and in the presence of reductants to the corresponding alcohols. Some of these materials were detected on proteins after complete enzymatic (Pronase) hydrolysis and LC/MS/MS quantification, providing direct evidence for peroxide formation on proteins. This approach may allow the quantification of protein modification in intact cells arising from singlet oxygen formation.