Effect of Impurities on the Matrix-Assisted Laser Desorption Mass Spectra of Single-Stranded Oligodeoxynucleotides

The effect of impurities on the analysis of single-stranded DNA oligomers by the technique of matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry has been studied using the matrix 3-hydroxypicolinic acid and 355-nm pulsed light. By mixing the DNA oligomers with different concentrations of impurities and recording mass spectra, limits are set on the tolerable level of a given impurity in a sample. The tolerance limits for sodium chloride, potassium chloride, sodium acetate, sodium fluoride, sodium dodecyl sulfate (SDS), and manganese(II) chloride were found to be approximately 10-2 M. It was found that magnesium salts degraded the mass spectrum at much lower levels of 10-4 M. The organic compounds tris(hydroxymethyl)aminomethane (Tris), urea, dithiothreitol (DTT), glycerol, and ethylenediaminetetraacetic acid (EDTA), when present as its ammonium salt, were tolerable at concentrations into the range of 0.25−0.5 M, while the organic polyamine compound spermine substantially degraded the mass spectrum at concentrations above 10-2 M. When comparing these results for DNA analysis with previously reported limits for protein analysis, large differences are seen for some of the impurities tested.