Aspects of the sequencing of carbohydrates and oligonucleotides by matrix-assisted laser desorption/ionization post-source decay.

The possibility of structural elucidation of carbohydrates and oligonucleotides by matrix-assisted laser desorption/ionization followed by post-source decay (MALDI-PSD) is investigated. Spectra of both classes of compounds exhibit the better signal-to-noise ratios for the intact species in the negative-ion mode, but the most informative spectra for structural elucidation by PSD are obtained in the positive-ion mode. A novel fragmentation mode is demonstrated on a model sialylated complex type N-linked oligosaccharide. Prompt fragmentation in the positive-ion mode can remove the sialic acids at high laser irradiance if a suitable matrix is used. The remaining sugar backbone is then characterized by post-source decay. A modified oligonucleotide is analyzed with 3-hydroxypicolinic acid as the matrix and ammonium tartrate to displace sodium. Enough structural information is obtained to verify the modification.