Tandem mass spectra of a variety of adenine‐containing deoxynucleic acid anions obtained using collisional activation in a quadrupole ion trap are described. Data are reported for singly charged mono‐, di‐ and trinucleotide species, and also for multiply charged anions derived from tri‐, tetra‐, penta‐ and hexanucleotides. Attention is focused on the first step in the unimolecular decomposition of these species, namely the loss of the nucleobase. Specifically, the competition between the loss of the nucleobase as a neutral versus its loss as an anion is addressed within the context of a proposed proton‐bound intermediate consisting of the nucleobase and a phosphodiester linkage. The data are interpreted on the basis of the energy surface involved in the break‐up of the proton‐bound intermediate, which can explain why the competition between loss of a neutral versus charged base is strongly dependent upon the charge of the parent ion.
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