Gas-phase fragmentation of oligonucleotide ions

The advent of ionization methods capable of forming gaseous oligonucleotide ions has made mass spectrometry a viable tool for structural studies of nucleic acids. Structural information regarding the primary sequence of a nucleic acid and the nature of its nucleobases via mass spectrometry has relied primarily on the dissociation behavior of ions formed by one or more of the available ionization methods. This review is focused on studies devoted to the fragmentation of oligonucleotide ions. In particular, it relates dissociation phenomenology observed over a wide range of ion types and dissociation conditions. Furthermore, it also relates the various mechanisms that have been proposed to account for the observed behavior. The review is organized along the lines of ionization method. While there is no fundamental reason to organize the review in this way, much of the discourse in the literature has evolved along these lines. The major ionization methods applied to nucleic acids have been fast atom bombardment, electrospray ionization, and matrix-assisted laser desorption ionization. It is apparent in reviewing the observations made to date that a wide range of reaction phenomenology has been observed for the different ion types and even for the same ions subjected to different activation conditions. It is also apparent that more than one dissociation mechanism can contribute, depending upon ionization conditions, ion polarity and charge state, and ion activation conditions. (C) 2004 Elsevier B.V. All rights reserved.