Mobile phase optimisation for oligonucleotide analytical methods by LC-MS

Supported by:

10 September 2020

Supported by:

10 September 2020


The use of alkylamine ion pair and perfluorinated alcohols in the analysis of oligonucleotides by LC-MS techniques has been the mainstay in characterisation and quantitation methods for synthetic oligonucleotides for decades. Often, analytical chemists default to relatively high concentrations of both, but how much ion pair is needed for optimal chromatographic performance and how much does perfluorinated alcohol concentration contribute to electrospray ionisation efficiency?

In this on-demand, we provide an overview of nucleic acid therapeutics and discuss the chromatographic challenges associated with oligonucleotides. We also explore modulation of the mobile phase additives alkylamine ion pair and perfluorinated alcohols. Finally, we will show how optimisation of mobile phase can improve not only chromatographic performance and MS sensitivity, but may also directly impact MS data acquisition, thus facilitating data analysis.

Learning outcomes of this webinar:

  • An overview of nucleic acid therapeutics
  • The chromatographic challenges associated with oligonucleotides
  • Method development considerations for oligonucleotide analysis by LC
  • The role of mobile phase and column chemistry in LC-MS methods for oligonucleotides
  • How to improve overall method robustness and sensitivity for oligonucleotide method development.


Brian Rivera, Senior Product Manager, Phenomenex

Brian Rivera is currently the Product Manager for Bioseparations Products at Phenomenex, Incorporated, Torrance, California, US. Prior to this role, Brian has held a variety of positions in sales and marketing related to biotechnology products. He worked as a Technical Sales Specialist for Phenomenex and Eppendorf, an Account Manager for ProZyme and a Biotechnology Product Specialist for Phenomenex. Prior to his business-facing roles, Brian worked in analytical methods development and in manufacturing support roles for a few biotechnology companies in the San Francisco Bay Area; including Avid Bioservices, ProZyme and Chiron Corporation. He has a bachelor’s degree from the University of California, Davis.

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