Oligonucleotide analysis

Leading the way in oligonucleotide bioanalysis and quantification

Oligonucleotides are exploding as a therapeutic modality. The ability of oligonucleotide therapies to modulate disease mechanisms at the messenger RNA (mRNA) level opens up the potential to treat pathologies previously considered “undruggable.”

The molecular properties of oligonucleotides place them somewhere between small molecules and protein therapeutics. SCIEX recognizes the special analytical challenges that oligonucleotide therapeutics present to scientists. We have partnered with scientists in the pharmaceutical and biopharmaceutical industries to develop precise, sensitive and efficient analytical solutions to help enable your investigational new drug (IND) or new drug application (NDA) programs.

Faster candidate selection and shorter development time for your oligonucleotides

Say goodbye to reinjecting or reanalyzing samples

Many existing oligonucleotide assays can be too rigid to adapt when problems arise. Explore flexible and compliant data analysis options that give you complete information from a single injection.


Oligonucleotide quantitation and characterization by high resolution LC-MS


Understanding oligonucleotides from every angle: utilizing mass spectrometry for characterization and quantification


High resolution LC-MS/MS solutions for oligonucleotides

Routinely reach pg/mL sensitivity and achieve lower detection levels

Discover a solution that provides extreme negative ion mode sensitivity and detection. Benefit from fewer required experiments, faster candidate selection and shorter development time.

Technical note

Improve sensitivity for antisense oligonucleotide quantification in plasma using microLC-MRM methodology

Technical note

Sensitive quantification of therapeutic oligonucleotides extracted from plasma

Technical note

Approaches for quantification of oligonucleotides in extracted plasma using high resolution mass spectrometry

Feel confident in quantification and identification of all mixed oligonucleotide species

Full length and truncated oligonucleotides with ligand binding assay formats are difficult to distinguish. With high resolution MS and MS/MS solutions, you can confirm the mass of full length and clipped or truncated oligonucleotides with confidence.

Technical note

High resolution analysis of synthetic oligonucleotides

Technical note

Analysis of locked nucleic acid (LNA) oligonucleotides (ON) and related impurities using accurate mass spectrometry

Technical note

Metabolite ID and relative quantification of oligonucleotides in plasma

Technical note

Characterization of oligonucleotides and related impurities to support the development of drug substances

Technical note

Development of an ultra-sensitive assay for anti-sense oligonucleotide quantification

Extreme sensitivity and maximum flexibility

The market-leading negative ion performance across our mass spectrometry portfolio delivers extreme sensitivity for your most challenging therapeutic oligonucleotides. You will see not only a boost in sensitivity with microflow chromatography, but also a decrease in system contamination and downtime for cleaning. Confidently run your analyses with the ease of connecting SCIEX sources and employing instrumentation designed specifically for microflow.

ZenoTOF 7600 system

Discover the power of Zeno trap pulsing with EAD fragmentation technology in this high-resolution accurate mass system.

Triple Quad 7500 LC-MS/MS system

Start detecting the previously undetectable and quantify at lower level with impressive precision.

TripleTOF® 6600+ LC-MS/MS System

Great negative ion mode performance with the ability to simultaneously quantify both analytes and metabolites.

SCIEX Triple Quad™ 6500+ LC-MS/MS System

Excellent negative ion mode performance ensures high sensitivity for the lowest levels of oligonucleotide qualification.

OptiFlow™ Quant Solution

Experience the intelligent union of high sensitivity, ease of use and robustness to quantify oligonucleotides.

SCIEX OS-Q Software

This compliant-ready solution is optimized for qualitative and quantitative data analysis.

Molecule Profiler software

Determine impurities and biotransformations for a wide variety of therapeutic molecules with highly accurate and flexible workflows.

Novatia ProMass

Automatically deconvolute multiply-charged ESI/LC/MS mass spectra from a wide variety of biomolecules.

Precision analytics for oligonucleotide, cell and gene therapy

As the technologies for manufacturing and analysis of gene therapy products continue to evolve, it’s important to keep up with industry trends and analytical advancements. This compendium can help you advance your gene therapies and oligonucleotide therapeutics to the next level with the latest tools and methods.

Oligonucleotide knowledge accelerator

Whether you need high sensitivity for quantification or to characterize impurities and catabolites, SCIEX has complete end-to-end solutions for fast, easy and confident LC-MS oligonucleotide analysis.