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 yields using matrices such as 2,5-dihydroxybenzoic acid and 3-hydroxy-4-methoxybenzaldehyde are enhanced by the addition of ammonium salts at a molar ratio of 1:1, pH 7. 3-Hydroxy-4-methoxybenzaldehyde was tested with 12 different ammonium, alkylammonium, and pyridinium salts for the ability to cocrystallize with oligodeoxynucleotides and to improve desorption and ionization. Ions of oligodeoxynucleotides 9, 10, and 11 nucleotides in length were observed with a matrix of 3-hydroxy-4-methoxybenzaldehyde and ammonium acetate, pH 7, at a mass resolution of 100-150 (fwhm). A small oligodeoxynucleotide (11-mer) was observed at the femtomole level with a combination of 2,5-dihydroxybenzoic acid and ammonium acetate as the matrix. Ions from single stranded DNA (60 nucleotides in length) were also observed using this same matrix combination. The results of these studies have shown that both sensitivity and desorption conditions need to be further improved before complex mixtures of large pieces of DNA can be effectively analyzed.