N-Hydroxylated polyamine derivatives were found to decompose during the ionization process of liquid chromatographyatmospheric pressure chemical ionization-mass spectrometry (LC-APCI-MS) experiments. The phenomenon was studied with a model compound, a synthetic N-hydroxylated tetraamine derivative. It was found that reduction, oxidation and water elimination occurred during APCI to generate the corresponding amine, N-oxide, and imine. The investigation further revealed that decomposition of hydroxylamines during APCI depends upon the concentration of the analyte and on the acidity of the solution introduced into the ionization source. The pH-dependence of decomposition was utilized for the development of an MS method that allows for the unambiguous identification of N–OH functionalities. This method was applied for the study of natural products including polyamine toxins fromthevenomof thespider Agelenopsis aperta and mayfoline, a cyclic polyamine derivative of the shrubMaytenus buxifolia. Copyright c 2009 JohnWiley & Sons, Ltd.