Electrospray tandem mass spectrometry of nucleotides.

The tandem mass spectra (MS/MS) following electrospray ionization of nucleotides (from 2- to 6-mers) have been examined under a range of collision and ionization conditions. In general, abundant peaks due to the free bases and phosphate groups are observed, along with a limited number of sequence ions. A number of strategies for increasing the extent of the observed fragmentation were investigated. Increasing the skimmer potential of the ion source, thereby increasing the initial internal energy of the incident ions, did not significantly enhance the sequence-specific fragmentation, although the relative intensities of fragment ions increased. In MS/MS spectra of different adducts (i.e. [M + H]+, [M-H]-) of dinucleotides the intensity of the ions due to the bases (BH2+ or B-) is dependent on both the base position (i.e. either 3' or 5') and the nature of the adduct ion. These data show that MS/MS spectra of [M-H]- ions of dinucleotides generated by electrospray ionization may be equally as diagnostic as MS/MS spectra obtained following fast-atom bombardment. With [M + Li]+ ions, more sequence ions were observed compared to the corresponding protonated and deprotonated species. For oligonucleotide hexamers, MS/MS spectra of the [M-2H]2- ions show fragment ions due to loss of bases followed by cleavage of the 3' C--O bond in the sugar from which the base is lost (i.e. w ions); however, a strong preference for loss of any particular base is not observed. Finally, MS/MS spectra of 5'-ApCpC-3' and 5'-d(AGGCCT)-3' obtained on a magnetic sector orthogonal acceleration time-of-flight mass spectrometer demonstrate the potential utility of this instrumental configuration for MS/MS analysis of oligonucleotides.