By Remco van Soest, Kerstin Pohl, Yunyun Zou and Elliott Jones, SCIEX
Oligonucleotide therapeutics and gene therapies are rapidly gaining attention as their potency improves and delivery challenges are addressed. Modalities such as antisense oligonucleotides (ASOs) are becoming more important due to their high specificity and ability to reach formerly undruggable targets. To ensure safe drugs, methods for the identification and characterization of the full length product (FLP) and impurities are critical. High resolution mass spectrometry (HRMS) can be used for the identification of potential impurities, by comparing the measured accurate masses and isotope patterns with those calculated. However, there is a lack of powerful yet intuitive processing software, and manual interpretation is cumbersome and time consuming. Furthermore, structural confirmation leveraging MS/MS adds an additional level of complexity.
Using the Molecule Profiler software to overcome these challenges, this technical note shows the identification and relative quantification of the 5’(n-1), 5’(n-2) and 5’(n-3) impurities of a fully phosphorothioated FLP spiked into an FLP sample at levels between 0.1 and 10% (w/w). The software can perform relative quantification based on TOF-MS, and assign fragment ions of the potential impurities to confirm their structures, facilitating the characterization of drugs in development.