Utility of organic bases for improved electrospray mass spectrometry of oligonucleotides

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Abstract
The sensitivity and accuracy of the mass spectrometric analysis of oligonucleotides using electrospray ionization can be compromized when the oligomer is adducted in the gas phase to cations such as sodium or potassium. We have evaluated the addition of mM concentrations of a series of organic bases with solution pKb values ranging from 11.5 to 5.5 and gas-phase proton affinities ranging from 213 to 232 kcal/mol as a method for suppression of signals from alkali-adducted ions. Stronger bases such as triethylamine and piperidine reduce the signals from bound sodium most effectively, but also decrease the total ion current from oligonucleotide. Imidazole, with a solution pH of ∼8.0, provides modest suppression of sodium/potassium adduct ions, but up to a four-fold improvement in sensitivity. Co-addition of imidazole and triethylamine or piperidine produces high ion abundance and good suppression of cation-adducted species for samples of phosphodiester or phosphorothioate oligomers which have not been desalted via preliminary precipitation or by high-performance liquid chromatography. Addition of high concentrations of imidazole generates a bimodal distribution of charge states, which may reflect different gas-phase conformations for single-stranded oligomers.

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