Simplified sample preparation for the analysis of oligonucleotides by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometr y (MALDI-TOFMS) for the analyses of oligonucleotides has generally been car ried out using negative ionisation conditions, usually following ammonium i on-exchange chromatography and the addition of ammonium buffers to the MALD I matrix. The molecular ion region is complex, due to the varying degrees o f ammoniation of the phosphate backbone of the oligonucleotide, This gives rise to an overall decrease in sensitivity compared with similar size pepti des and can cause ambiguity of assignment of the relative molecular mass of the sample, This study describes the use of H+ ion exchange resin in situ as the means of removing alkali metal ions from the phosphate backbone of t he oligonucleotide. An increase in resolution, sensitivity and identificati on of the molecular species is reported, with little or no difference in se nsitivity observed between positive or negative ionisation spectra. This me thod is now used for routine screening of synthetic oligonucleotides with a gain in sensitivity of 1-2 orders of magnitude compared with previous meth ods, and mass assignment errors of +/-0.1% are routinely recorded for exter nally calibrated data. Copyright (C) 1999 John Wiley & Sons, Ltd.