Ion trap collisional activation of the deprotonated deoxymononucleoside and deoxydinucleoside monophosphates.

Deoxymononucleoside and deoxydinucleoside monophosphate anions formed by electrospray have been subjected to ion trap collisional activation. The threshold for decomposition via loss of base is significantly lower for the deoxymononucleoside 3'-monophosphates than for the corresponding 5'-monophosphates, which indicates that the presence of a charged 3' phosphate group facilitates base loss. The behavior of the bases among each class of isomers shows slight variation in threshold and tandem mass spectrometry efficiency with tile notable exception of 2'-deoxyguanosine 5'-monophosphate. This ion is exceptionally stable toward decomposition via base loss, which reflects a strong hydrogen bonding interaction between the base and the phosphate group. All dinucleotides fragment via similar mechanisms, but the propensity for neutral base loss relative to loss of a charged base is highly dependent on the identities of both the 5' and 3' bases. The behavior of the dinucleotides under collisional activation conditions supports the proposal that base loss proceeds via a proton-bound dimer intermediate in which loss of the charged base directly competes with loss of the neutral base. Application of the kinetic method allows for quantitative predictions of the differences of the gas-phase acidities of the dimer components.