Identification of Modified Nucleosides by Secondary-Ion Mass Spectrometry

Argon ion bombardment of nucleosides produces mass spectra of high quality from which the molecular weight and the nature of the sugar can readily be determined. The most intense peak corresponds to the base itself, and ions representing the base attached to Na super(+), or other cations, are obtained by addition of the appropriate salt. Parallels with fragmentations observed in electron impact exist and help to define molecular structures. Detection limits of a few nanograms are demonstrated and it is shown that ions characterizing the base can be greatly enhanced by simple acid pretreatment of the sample. Comparisons are made with pyrolysis mass spectrometry/mass spectrometry and it is concluded that modified bases cannot be identified in intact DNA by pyrolysis MS/MS without the possibility of isomerization although MS/MS does provide isomer specificity for pure modified bases.