Collision-induced dissociation of cytidine and its derivatives

The collision-induced dissociation of adenosine, uridine and guanosine, and their corresponding nucleobases has been published previously.1-3 Here we report the collision-induced dissociation of cytidine and the elucidation of its fragmentation pathways using stable isotope-labeled cytidines, through a quadrupole ion trap for tandem mass spectrometry up to MS(4). Furthermore, we investigated the collision-induced dissociation of five cytidine derivatives: 3-methylcytidine, N(4)-methyl-2'-deoxycytidine, 5-methylcytidine, 2-thiocytidine and N(4)-acetylcytidine. The primary fragmentation pathway was the neutral loss of ribose. MS(3) on the retained nucleobase generally resulted in an intense signal from the elimination of ammonia, but also in fragment ions characteristic of the different cytosine derivatives. On the basis of the MS(n) data, fragmentation pathways and plausible mechanisms are suggested.