In the collisionally-activated dissociation of the proton-bound cluster ions of DNA base guanine (G) and cytosine (C), $G{ullet}{ullet}H^+{ullet}{ullet}C$, the abundance of [$CH^+$] ions was found to be higher than that of [$GH^+$] despite the fact that G has a higher proton affinity than C. This unexpected observation seems to demonstrate another example that the simple kinetic method scheme does not work. We suggest that a kinetic factor or detailed dynamics governing the proton transfer and dissociation should be carefully considered in the applications of the kinetic method to the proton affinity measurements.