Characterization of Oligodeoxynucleotide Fragmentation Pathways in Infrared Multiphoton Dissociation and Electron Detachment Dissociation by Fourier Transform Ion Cyclotron Double Resonance

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 pr...