The term reactive oxygen species refers to small molecules that can oxidize, for example, nearby proteins, especially cysteine, methionine, tryptophan, and tyrosine residues. Tryptophan oxidation is always irreversible in the cell and can yield several oxidation products, such as 5‐hydroxy‐tryptophan (5‐HTP), oxindolylalanine (Oia), kynurenine (Kyn), and N‐formyl‐kynurenine (NFK). Because of the severe effects that oxidized tryptophan residues can have on proteins, there is a great need to develop generally applicable and highly sensitive techniques to identify the oxidized residue and the oxidation product. Here, the fragmentation behavior of synthetic peptides corresponding to sequences recently identified in three skeletal muscle proteins as containing oxidized tryptophan residues were studied using postsource decay and collision‐induced dissociation (CID) in matrix‐assisted laser desorption/ionization (MALDI) time‐of‐flight (TOF)/TOF mass spectrometry (MS) and CID in an electrospray ionization (ESI) double quadrupole TOF‐MS. For each sequence, a panel of five different peptides containing Trp, 5‐HTP, Kyn, NFK, or Oia residue was studied. It was always possible to identify the modified positions by the y‐series and also to distinguish the different oxidation products by characteristic fragment ions in the lower mass range by tandem MS. NFK‐ and Kyn‐containing peptides displayed an intense signal at m/z 174.1, which could be useful in identifying accordingly modified peptides by a sensitive precursor ion scan. Most importantly, it was always possible to distinguish isomeric 5‐HTP and Oia residues. In ESI‐ and MALDI‐MS/MS, this was achieved by the signal intensity ratios of two signals obtained at m/z 130.1 and 146.1. In addition, high collision energy CID in the MALDI‐TOF/TOF‐MS also permitted the identification of these two isomeric residues by their v‐ and w‐ions, respectively. Copyright © 2011 John Wiley & Sons, Ltd.