Investigation of oligonucleotide fragmentation with matrix-assisted laser desorption/ionization Fourier-transform mass spectrometry and sustained off-resonance irradiation.

Matrix-assisted laser desorption/ionization (MALDI) can be combined with Fourier-transform ion cyclotron resonance mass spectrometry (FTMS) for the detailed structural examination of biomolecules such as peptides and oligonucleotides. We have been able to detect molecular ions for bovine heart cytochrome c (MW = 12,327) by MALDI-FTMS (355 nm laser desorption, 2,5-dihydroxybenzoic acid matrix). Although the mass resolution of these molecular ions is poor, the experiments verify that the MALDI-FTMS mass range for our 3-tesla instrument is in excess of m/z 12,000. Accurate mass measurements and selective dissociation experiments were used to examine the fragmentation pathways of small oligonucleotides in detail. Sustained off-resonance irradiation (SORI) was found to be superior to conventional on-resonance collisionally activated dissociation (CAD) for the efficient dissociation and detection of fragment ions for oligonucleotides. These experiments indicated that oligonucleotide fragmentation is a complex process and results not only from simple elimination of nucleic bases and cleavages of phosphate ester bonds, but also by rearrangement processes in which a terminal phosphate moiety can be transferred to an internal phosphate group.