Frit-Fast Atom Bombardment Liquid Chromatography/Mass Spectrometry, a Useful Method for Sequencing Dinucleotides

Directly combined liquid chromatography/mass spectrometry (LC/MS) based on thermospray ionization has proved to be a rapid and efficient method for detection and characterization of post-transcriptionally modified nucleosides from tRNA. However, when unexpected components encountered in the event are dinucleotides of the type NpN', which may be formed principally due to marked resistance of some modified residues to nuclease digestion, some difficulties arise in the identification. In thermospray LC/MS, dinucleotides usually do not produce molecular ion and sequence-related ion species, but produce the corresponding base and nucleoside ions instead. Therefore, we can know the constituent nucleosides, but cannot determine either dinucleotide being NpN' or N'pN from the mass spectrum. In this report, we describe a successful attempt for differentiation of such isomeric dinucleotides by using LC/MS interfacing continuous-flow frit-fast atom bombardment (frit-FAB) ionization.