Evaluation of mobile phase composition for enhancing sensitivity of targeted quantification of oligonucleotides using ultra-high performance liquid chromatography and mass spectrometry: Application to phosphorothioate deoxyribonucleic acid

•Proposed mechanisms for sensitivity changes with mobile phase composition.•Enhanced LC–MS sensitivity for oligonucleotides by two orders of magnitude.•Novel extraction method for oligonucleotide bioanalysis with >75% recovery. LC–MS based assays are a promising approach for the bioanalysis of oligonucleotide therapeutics due to their selectivity and structure identification capabilities. However, the lack of sensitivity and complicated sample preparation procedures remain a barrier for application of LC–MS based assays to preclinical and clinical studies. Numerous studies have shown that the mobile phase composition, especially organic solvent type, has a significant impact on the MS sensitivity of oligonucleotides. In this study, we systematically investigated the type of organic solvents and concentration of organic modifiers for their effect on electrospray desorption efficiency, chromatographic separation and LC–MS signal intensity and provide mechanisms for these effects. 25mM HFIP, 15mM DIEA and the use of ethanol as an organic solvent were observed to achieve a two order of magnitude increase in LC–MS signal intensity when compared to the most commonly used LC–MS mobile phase composition. Phenol–chloroform LLE in combination with ethanol precipitation was demonstrated to be effective for quantitative bioanalysis of therapeutic oligonucleotides. Various conditions for ethanol precipitation were evaluated and >75% absolute recovery was achieved using an optimized extraction procedure. No increase in column pressure or deterioration of separation was observed for >500 injections of biological samples. The method run time was 5min and the LOQ was 2.5ng/ml. The accuracy (% error) and precision (%RSD) are