Collision-induced dissociation of polyprotonated oligonucleotides produced by electrospray ionization

The efficient production of polyprotonated oligonucleotides, studied at n < or = 19, occurs from water/propan-2-ol solutions over an ammonium acetate concentration range between 2.5 and 40 mm and a pH range from 5 to 11. Average charge-state levels observed were approximately half of those found in mass spectra of polyanionic oligonucleotides, reflecting differences in sites of ionization: heterocyclic bases for protonation and phosphodiester backbone for deprotonation. Collision-induced dissociation mass spectra show three principal reaction paths: (1) release of protonated bases, with abundances dictated largely by base proton affinity; (2) phosphodiester chain cleavage at C3'-O3' indicative of sequence in the 3'-->5' direction; and (3) chain cleavage concomitant with base loss giving furan-type ions indicative of sequence in the 5'-->3' direction, analogous to reactions of polyanionic oligonucleotides. Thymine residues undergo very little protonation, resulting in characteristic absence of phosphodiester cleavage on the 3' side of T sites, producing mass-ladder gaps representing dinucleotides.