Trimethylborate (TMB) reacts with deprotonated monomer, homo-, and heterodimer ions of nucleotides (2′-deoxyadenosine-5′-monophosphate [dAMP], 2′-deoxycytidine-5′-monophosphate [dCMP], 2′-deoxyguanosine-5′-monophosphate [dGMP], and 2′-deoxythymidine-5′-monophosphate [dTMP]) in a quadrupole ion trap mass spectrometer by addition with concomitant elimination of one or two methanol molecules (monomers), one or three methanol molecules (homodimers), and three methanol molecules (heterodimers). The mode of reaction appears to influence the observed rates, with the loss of only one methanol molecule corresponding to the fastest rate. There appears to be a structure–reactivity correlation for the monomers, with the [dGMP – H]– ions (which adopt a syn conformation of the guanine moiety) reacting fastest with TMB through the loss of only one methanol molecule. No such structure–reactivity trends are observed for the homo- and heterodimers. In addition, the collision-induced dissociation (CID) reactions of the [(dXMP)n − H]– (n = 1 or 2) as well as the [dXMP + dYMP – H + (CH3O)3B – 3(CH3OH)]– ions (where nucleotides X, Y = A, C, G, or T) were studied. The latter fragment to form [dXMP – H + BPO4]– and [dXMP – 3H + BPO3]– ions (where X = A, C, G, or T), while [dXMP – H]– ions fragment by neutral base loss. The homo- and heterodimers fragment to form [dXMP – H]– and [dXMP + HPO3]– ions, and the relative abundances of the [dXMP – H]– monomer ions from the heterodimers led to the following acidity order: dGMP ≈ dTMP > dCMP > dAMP.
Collision-Induced Dissociation (CID) Spectra versus Collision Energy Using a Quadrupole Ion Trap Mass Spectrometer IV -Dissociation of Ionized Maleamide and Fumaramide-