The synthesis of positively charged and mass tagged nucleosides containing
a quaternary ammonium functionality within the penultimate position of a pr
imer is described. Neutralization of the sugar/thiophosphate backbone by al
kylation increases the detection sensitivity in the mass spectrometric anal
ysis by a factor of at least 100. The variable introduction of these novel
compounds within the extension primers enables flexible design of multiplex
genotyping reactions.