Collisionally activated dissociation of protonated 2′-deoxycytidine, 2′-deoxyuridine, and their oxidatively damaged derivatives

Abstract

We examined the collisionally activated dissociation (CAD) pathways of protonated 2=-deoxycytidine (dC), 5-formyl-2=-deoxycytidine (5-FmdC), 5-hydroxy-2=-deoxycytidine (5-OHdC), 5-hydroxymethyl-2=-deoxycytidine (5-HmdC), and their corresponding stable isotope-labeled compounds to gain insights into the effects of modifications on the fragmentation pathways of the pyrimidine bases. Multi-stage MS (MS n ) results showed that protonated cytosine, its 5-hydroxyland 5-hydroxymethyl-substituted derivatives, but not its 5-formyl-substituted analog, could undergo Dimroth-like rearrangement in the gas-phase. The elimination of HNCO was one of the major fragmentation pathways observed for the protonated ions of all dC derivatives except for 5-hydroxymethylcytosine, which underwent this loss only after a H 2 O molecule had been eliminated. In addition, the protonated cytosine and 5-hydroxycytosine can undergo a facile elimination of NH 3 molecule. This loss, however, was not observed for protonated 5-hydroxymethylcytosine, 5-formylcytosine, and their uracil analogs. Taken together, our study demonstrated that modifications could alter markedly the CAD patterns of the protonated pyrimidine bases. The results from this study provided a basis for the identifications of other modified pyrimidine bases/nucleosides by tandem mass spectrometry. (J Am Soc Mass Spectrom 2006, 17, 1335-1341

Identification of 5-Hydroxycytidine at Position 2501 Concludes Characterization of Modified Nucleotides in E. coli 23S rRNA

“…15 We compared these data with reported MS n experiments on various (deoxy)cytidine modifications and found that the fragmentation pattern of the nucleobase at m/z 128 in MS 3 was qualitatively, as well as quantitatively, similar to that reported by Cao and Wang on the nucleobase of 5-hydroxy-2′-deoxycytidine. 16 Subsequent MS 4 fragmentation on the ions at m/z 111, 101, and 100 ( Fig. S1) was in agreement with the similar MS 4 data reported by Cao and Wang.…”

Study of forced decomposition behavior of lamivudine using LC, LC–MS/TOF and MSn

“…The ion of m/z 94 resulted from neutral loss of water from cytosine, which is also reported previously [17]. There were two possible structures for the ion of m/z 69, as shown in the scheme.…”

A Nano-Chip-LC/MSn Based Strategy for Characterization of Modified Nucleosides Using Reduced Porous Graphitic Carbon as a Stationary Phase

“…MS 4 of m/z 100, the most intense ion from MS 3 , gave product ions of m/z 72 and 57 corresponding to loss of CO and HNCO, respectively. This online MS 4 fragmentation pattern is identical to the one observed for m/z 100 of the nucleobase of oh 5 dC in a direct infusion experiment reported by Cao and Wang [40].…”