The reaction of singlet oxygen (1O2) with the amino acids tryptophan and tyrosine, either free or inserted in peptides or proteins, gives rise to hydroperoxides. To understand the impact of these hydroperoxides in complex biological systems, methods allowing their characterization and accurate quantification must be available. In this work, hydroperoxides derived from tryptophan and tyrosine and from peptides containing these amino acids were synthesized by photooxidation, and characterized by high‐resolution mass spectrometry. In addition, experiments were carried out to compare two colorimetric methods commonly used for quantification of peroxides, namely the iodometric and the ferric‐xylenol orange assays. For the tryptophan hydroperoxide, the quantifications obtained by colorimetric methods were then compared to that obtained by NMR. The results showed that for the ferric‐xylenol orange method, the stoichiometry between peroxide and Fe3+ ions varies considerably. On the other hand, for the iodometric assay, the stoichiometry peroxide:I3− ions is always 1:1. However, the kinetics of the reactions of peroxides with I− vary, and the assay must be performed in anaerobic conditions. Thus, the iodometric method is more appropriate for precise quantification of a given peroxide. The characterization and accurate quantification of biological peroxides is key to understand the mechanisms involved in redox processes.