Tandem Mass Spectrometry of Small, Multiply Charged Oligonucleotides

Multiply charged anions derived from electrospray ionization of the sodium salts of various small oligonucleotides (n = 4−8) have been subjected to tandem mass spectrometry (MS/MS) in a quadrupole ion trap. All ions were observed to dissociate with high efficiencies even under conditions not ordinarily conducive for the observance of high MS/MS efficiency. Large fractions of the total product ion signal could be attributed to single-cleavage reactions with the parent ion charge shared among the two product ions in various combinations. In every case, the most facile reaction was observed to be the loss of the adenine anion. This reaction was then observed to be followed by cleavage of the 3′ C–O bond of phosphodiester linkage of the sugar from which the adenine had been lost.