Infrared multiphoton dissociation (IRMPD) is a vibrational excitation tandem mass spectrometric fragmentation method valuable for sequencing of oligonucleotides. For oligodeoxynucleotides, typical product ions correspond to sequence- specific 5′ (a–base) and their complementary 3′ w-type ions from carbon–oxygen bond cleavage at the 3′ position of the deoxyribose from which a nucleobase is lost. Such fragmentation patterns are also observed in collision activated dissociation (CAD). The CAD oligodeoxynucleotide fragmentation mechanism has been characterized in detail. By contrast, fragmentation schemes in IRMPD have not been rigorously established. In this paper, we apply, for the first time, Fourier transform ion cyclotron double resonance (DR) experiments to characterize IRMPD fragmentation pathways of oligodeoxynucleotide anions. Our results suggest that neutral base loss precedes backbone fragmentation but that T-rich oligodeoxynucleotides fragment via a different mechanism, similar to the mechanisms proposed for CAD. We also extend the DR approach to characterize intermediates in electron detachment dissociation of hexamer oligodeoxynucleotides. Here, we found that charge reduced radical precursor ions constitute major intermediates for dT₆, d(GCATAC) and d(GCATGC). Furthermore, (a/z–T) ions (z ions correspond to C–O bond cleavage on the other side of a backbone phosphate group as compared to the formation of a ions) mainly originate from secondary fragmentation of a/z radical ions for the oligodeoxynucleotide dT₆.

Keywords: IRMPD, infrared multiphoton dissociation, EDD, electron detachment dissociation, Fourier transform ion cyclotron resonance, ICR, FT- ICR, mass spectrometry, FT-MS, electrospray, ESI, oligonucleotide, DNA, fragmentation pathway, double resonance