ANALYSIS OF OLIGODEOXYNUCLEOTIDES BY NEGATIVE-ION MATRIX-ASSISTED LASER-DESORPTION MASS-SPECTROMETRY

Thirty compounds were tested in combination with ammonium acetate for the ability to desorb and ionize oligodeoxynucleotides by ultraviolet matrix-assisted laser desorption mass spectrometry. Negative ion yield s using matrices such as 2,5-dihydroxybenzoic acid and 3-hydroxy-4-met hoxybenzaldehyde are enhanced by the addition of ammonium salts at a m olar ratio of 1:1, pH 7. 3-Hydroxy-4-methoxybenzaldehyde was tested wi th 12 different ammonium, alkylammonium, and pyridinium salts for the ability to cocrystallize with oligodeoxynucleotides and to improve des orption and ionization. Ions of oligodeoxynucleotides 9, 10, and 11 nu cleotides in length were observed with a matrix of 3-hydroxy-4-methoxy benzaldehyde and ammonium acetate, pH 7, at a mass resolution of 100-1 50 (fwhm). A small oligodeoxynucleotide (11-mer) was observed at the f emtomole level with a combination of 2,5-dihydroxybenzoic acid and amm onium acetate as the matrix. Ions from single stranded DNA (60 nucleot ides in length) were also observed using this same matrix combination. The results of these studies have shown that both sensitivity and des orption conditions need to be further improved before complex mixtures of large pieces of DNA can be effectively analyzed.