Separation of PS diastereomers in GalNAc-conjugated siRNA—a comparative study of chromatographic and ion mobility mass spectrometry approaches

The separation and characterization of phosphorothioate (PS) diastereomers in GalNAc-conjugated siRNA presents a significant analytical challenge due to the high number of isomers present. To tackle this challenge, we explore and optimize various separation techniques, including chromatographic methods (ion-pair reversed-phase, anion exchange, and hydrophilic interaction liquid chromatography) and ion mobility mass spectrometry (IMS) to assess their efficacy in diastereomer separation. Our results indicate that AEX provides the highest diastereomer selectivity among the chromatographic techniques, although none achieved complete diastereomer separation for the chosen antisense and sense strand reference compounds. IMS, applied within a fragment-based tandem mass spectrometry approach, allows separation of all diastereomers of the antisense strand and partial resolution of the sense strand in the gas phase. The comparison of relative LC-UV quantification with IMS data reveals a strong correlation and suggests that IMS can effectively characterize diastereomer ratios not only qualitatively but also quantitatively, establishing IMS as a promising complementary analytical technique for diastereomer separation besides more established LC-UV methods.