Webinar 2D LC/MS: Peak purity determination for denaturing SAX oligonucleotide methods

About the webinar

Oligonucleotides are emerging new therapeutic entities, and reliable selective analytical methods to determine their purity and related impurities are critical. In this webinar, we present an innovative 2D LC-MS method for purity determination of oligonucleotides using denaturing methods. We also discuss oligonucleotide structure, typical impurities, and chromatographic methods including strong anion exchange (SAX) and ion-pairing reversed phase (IPRP) methods.

Key takeaways

• SAX peak purity cannot be reliably determined from UV chromatography alone. The chromatogram’s non-volatile salt-based eluents are not directly compatible with mass spectrometry, meaning potentially co-eluting impurities may remain undetected without an additional analytical step.
• A 2D-IPRP-MS workflow makes direct peak purity assessment possible. The approach fractions the target peak from SAX chromatography before transferring it to an MS-compatible IPRP method.
• A siRNA case study confirmed that chromatographic separation does not necessarily confirm true peak purity, after analysis of the duplex API showed that the SAX fraction still contained impurities.
• The technique is a development and method-evaluation tool and it should be used to assess whether an orthogonal SAX method is sufficiently selective and to investigate impurity peaks.

About the speakers

Marion Fresch, PhD
Senior Scientist QC

Marion Fresch is Senior Scientist in the QC Early Phase department at Bachem AG. She joined the company in 2021, specializing in HPLC method development, validations, forced degradation studies, release analytics, and stability testing for oligonucleotide NCE projects. Marion holds a PhD in analytical food chemistry from the University of Stuttgart, where her interest in patient health grew as she was working on food allergen analysis.

Claire Meyer, PhD
CMC Project Manager

Claire Meyer holds an MSc in Chemistry & Biology from the University of Strasbourg and a PhD in Chemistry from the University of Basel. She completed her postdoctoral research in Bioengineering at the University of California. Claire began her career as a Proposal Manager in a Biologics CDMO before joining Bachem, where she has spent the past 2.5 years focusing on oligonucleotides, transitioning from proposal management into project management. Her expertise spans early-phase CMC for oligos, while driving continuous improvement initiatives.