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Oligonucleotide MS

LC-MS Characterization of Oligonucleotides

Our methods are fast, cost-effective, and informative. We offer routine analyses in either a high-throughput mode to confirm the molecular weight of target oligonucleotide species, or a detailed LC-MS mode that utilizes high resolution chromatographic separation to identify impurities.

Features and Benefits of Novatia Oligo LC/MS Analysis Services:

  • Excellent mass accuracy, typically ± 0.01% for our standard ESI/MS analysis
  • Exact mass determination is also available with ppm-level (parts-per-million) accuracy on our high resolution mass spectrometers (orbitrap and QTof)
  • High quality results for larger (>50 base) oligonucleotides
  • High throughput MW determination/confirmation
  • “Soft” ionization allows analysis of DMT-on and other oligos with labile chemical moieties
  • Detailed LC/UV/MS analysis for component profiling
  • ProMass ESI spectral deconvolution technology
  • Unique, easy-to-use, web-based results reports
  • Very attractive pricing!
  • Industry-leading turnaround on results!  Results are typically returned the same or next day on most analyses.
  • We also specialize in protein LC/MS characterization.

Novatia offers nominal and high resolution ESI-MS methods for molecular weight confirmation of oligonucleotides.

Click here to to view demo data.

Novatia offers LC-UV-MS methods for detailed impurity profiling of oligonucleotides <80 bases. These methods are compatible with unmodified and modified (including PEGylated) oligonucleotides.

Click here to view demo data for our 5 min LC-UV-MS method and data processing options.

Novatia utilizes high resolution mass spectrometry and our novel deisotoping and charge deconvolution software for MS-based oligonucleotide sequencing. Our method can be used to reliably confirm the sequence of DNA and RNA, including modified oligos, up to ~40 bases. Applications include sequence confirmation of known sequences, as well as denovo sequencing and identification of modified residues.

ProMass Oligo Sequencing Tool transforms raw HCD MS/MS data into an easily interpretable sequence coverage chart with excel report.

See our full page highlight for more details.

Novatia offers LC-MS analysis of PEGylated oligonucleotides on our high resolution mass spectrometers (orbitrap or QTof) using our ProMass Deconvolution technology. This analysis can reveal:

1. The molecular weight distribution of a PEGylated oligo

2. Amount of free oligo present in sample

3. Lot-to-lot consistency across multiple samples

ESI mass spectrum (raw data):Deconvoluted Mass Spectrum (processed data):
PEGylated oligo, raw electrospray dataPEGylated oligo, deconvoluted data

Contact us for more information.

Novatia can perform oligo metabolite identification on your therapeutic oligonucleotide compounds. Based on the clients needs, single stranded or duplex oligos are incubated in biological matrices. At various timepoints throughout the incubation, oligos are extracted from the matrices and analyzed by high-resolution mass spectrometry. Novatia’s unique ProMass HR deconvolution software is then used track disappearance of the parent compound and identify the appearance of any metabolites over the time course of the incubation.

Nucleoside triphosphates (NTPs), including chemically modified NTPs, are important compounds in cellular and molecular biology research.  Novatia uses a volatile ion pairing buffer that allows for high fidelity characterization of these compounds and their impurities by LC/UV/MS in the negative ion mode.  Analyses can be performed in either nominal or accurate mass analysis modes.