The use of mass spectrometry coupled with chemical cross-linking of proteins has become one of the most useful tools for proteins structure and interactions studies. One of the challenges in these studies is the identification of the cross-linked peptides. While lysine and cysteine cross-linked peptides have been investigated, identification of fragmentation patterns of dityrosine cross-linked peptides is yet to be understood. Oxidative stress is known to play a key role in the neurodegenerative disease like Alzheimer’s disease (AD) and dityrosine in the amyloid plaques in AD brain is a potential biomarker of oxidative stress. Dityrosine cross-linked amyloid beta has been investigated in vitro to be toxic but whether its presence in the AD brain has any correlation with the disease progression and neurodegeneration is not well established. A quantitative analysis of covalently cross-linked dityrosine amyloid beta in AD brain using mass spectrometry requires a thorough understanding of the fragmentation pattern of these peptides. In this study we have investigated and characterized the fragmentation pattern of the LysC cleaved synthetically prepared amyloid beta(1-42) using ESI-MS/MS. In this study we report a detailed fragmentation study of the dityrosine containing peptide Aβ(1-16) generated by various techniques such as CID, HCD, ETD and ECD.  The fragmentation features observed here can be helpful in the interpretation and identification of cross-linked dityrosine peptides present in nature and can be further implemented in search engine's algorithms.