Quantitative proteomics has become an important method in modern life sciences. Besides protein identification, the aspect of quantification is of rapidly increasing relevance. MeCAT (metal-coded affinity tagging) is able to provide a tool that enables relative as well as absolute quantification. For structural elucidation, knowledge on the fragmentation behavior of MeCAT-modified peptides is highly beneficial. Therefore, the fragmentation behavior of MeCAT-labeled peptides under collision induced dissociation (CID), electron capture dissociation (ECD) and infrared multiphoton dissociation (IRMPD) conditions was studied. Application of CID and ECD allowed a straight-forward sequence elucidation of MeCAT-labeled peptides. During IRMPD all MeCAT-labeled peptides form characteristic fragments resulting from the fragmentational cleavage of the tagging group, thus, providing a screening method for the identification of labeled compounds. Furthermore, occurring side reactions during the labeling process were investigated. By-products were structurally characterized and reaction conditions were optimized in order to prevent the formation of these. Copyright © 2009 John Wiley & Sons, Ltd.