Matrix-assisted laser desorption fourier transform mass spectrometry for the structural examination of modified nucleic acid constituents

Laser desorption Fourier transform mass spectrometry (LDFTMS) can be used for the structural characterization of modified nucleic acid constituents. Laser desorption of these polar non-volatile compounds generates characteristic negative ions including abundant (M-H)^- ions in most cases. The accurate mass measurement and ion manipulation techniques available with FTMS provide detailed structural information for the identification of modified nucleic acid constituents such as amino-polycyclic aromatic hydrocarbon adducts of guanine at the isomeric level. Matrix-assisted laser desorption was required for the generation of abundant (M-H)^- ions as well as fragment ions of modified nucleotides and oligonucleotides. Examination of fragment ions from these compounds provided not only adduct identification and location but also sequence information and isomeric differentiation for most small oligonucleotides. In order to investigate the application of this instrumental technique to larger oligonucleotides, experiments were designed to examine the kinetic energy distributions of ions generated by matrix-assisted laser desorption and to evaluate methods of improving the trapping efficiencies. Initial experiments indicated that ions at m/z < 600 have kinetic energies less than 5eV; however, the use of simple retarding fields did not significantly affect trapping efficiencies, implying that the space-charged ion could generated by matrix-assisted laser desorption was relatively unaffected by small retarding fields (less than 10 V).