Avoiding Adducts: Improving Oligonucleotide MS Data Through Ion Source Optimization

Oligonucleotide analysis has become increasingly important in recent years following the successful introduction of mRNA vaccines and synthetic short interfering RNA (siRNA) therapeutics. The linear and highly charged nature of synthetic DNA and RNA presents inherent analytical challenges in mass spectrometry, particularly when trying to deconvolute polyvalent ion spectra. These challenges are further compounded by the presence of amine ion pairs, metal adducts, and mobile phase adducts, which leads to multiple split signals which complicates qualitative and quantitative analysis.

To combat these challenges, we will discuss optimization of ion-source conditions, including adjustments to pre-quadrupole voltage, interface voltage, de-solvation temperature, de-solvation line temperature, and gas flow rates for nebulizing, drying and heating gasses. The resulting method demonstrates a notable reduction in common mobile phase adducts associated with ion-pairing reverse-phase separation, while simultaneously increasing the total ion intensity of the non-adduct analyte signal.