Phosphatidylethanolamines (PEs) are abundant lipid constituents of the cellular membrane. The amino group of PEs exhibits high reactivity with hypochlorous acid that is generated under inflammatory conditions in vivo. The analysis of the resulting PE mono- and dichloramines is of significant interest since these species represent important mediators of lipid peroxidation. We have shown in a previous communication that mass spectrometric detection of PE chloramines is only possible with ESI MS, whereas MALDI-TOF MS fails to detect these products if standard matrices are used. In this work we demonstrate that the detection of PE chloramines is also possible by MALDI-TOF MS if 4-chloro-alpha-cyanocinnamic acid is used as matrix. The underlying processes leading to ionization of these species will be discussed in detail. Both, experimental and theoretical studies taking into account possible intramolecular rearrangements were performed to clarify these aspects.