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Oligo HTCS

Introducing the first fully-automated systems for oligonucleotide LC/MS!

The Oligo HTCS family of instruments are the only LC/MS systems designed to automate every aspect of oligonucleotide mass spectral analysis. The HTCS takes care of sample injection, desalting, detection, as well as data processing and reporting. With a sample throughput of up to 3000 samples/24 hrs, no LC/MS system on the planet is as productive as the Oligo HTCS. The HTCS allows you to characterize long (>120mers) or fragile oligos that are not amenable to MALDI-ToF. In fact, the HTCS is the only fully-automated MS system which can effectively QC oligos to be used in longmer DNA microarrays. Just as easily, the HTCS can also perform detailed LC/UV/MS profiling on your high-value oligos to give you full information about impurities, degradants, and failure products. Our ProMass software ties it all together, allowing you to process and communicate your results effortlessly.

For questions or to contact us about the Oligo HTCS, email us at

Download the Oligo HTCS brochure (PDF)

Applications include:

  • Oligonucleotide manufacturing quality control
  • Diagnostic oligonucleotides
  • Oligo therapeutics
  • RNA and RNAi
120-mer oligo spectrum 96-well plate view and mass spectrum of a 120-mer oligo acquired with the Oligo HTCS
Mass = 37031 Da, Mass Error = 0.6 Da

System Highlights

A choice of system configurations is available. Simply choose an appropriate system that is matched to your throughput, applications, and budget requirements.

  • The standard Oligo HTCS Vanquish is truly a unique system for oligonucleotide analysis. The system has a maximum injection rate of 40 sec/sample in high-throughput mode (~2000 samples over 24 hrs), and also has the flexibility to be automatically switched from high-throughput to detailed LC/MS profiling mode from within a sample list run.
  • The Oligo HTCS DHR is designed for those who need the highest possible throughput and highest quality in oligonucleotide mass analysis. The DHR system employs the new CTC PAL3 DHR dual-arm autosampler to achieve an injection rate of less than 25 sec/sample, which results in a total throughput of >3000 samples/24 hrs in mass confirmation mode.

Features & Benefits

All of our Oligo HTCS systems offer the following:

  • Analyze oligos from n=1 to n>120 bases in length
  • Analyze oligos that are difficult or impossible to analyze by MALDI-ToF, including long oligos (>50 bases), oligos with labile chemical moieties (e.g., BHQ’s), poly-T’s, hairpin oligos, etc.
  • Perfect for the QC of long oligos to be used in DNA microarrays or other applications
  • Analyzes both DNA and RNA oligos, particularly useful for analysis of siRNA oligos, including duplex oligos containing high salt concentrations
  • Routine mass accuracy of 0.01% (1 Da in 10 kDa) across entire mass range of oligos analyzed for isotopically unresolved mass spectra.  With new Orbitrap Exploris MX HRMS system, mass accuracy of 3 ppm or better is achieved for isotopically resolved mass spectral data.
  • Automated analysis includes built-in desalting for each oligo analyzed
  • Maximum throughput ~2000 samples/24 hrs (~3000 samples/24 hrs with DHR configuration)
  • Less expensive to operate (per sample) than high-throughput chip-based MALDI-ToF systems
  • Detailed profiling mode provides full information about impurities, failure sequences, and degradants
  • ProMass software processes entire sample lists without user intervention. ASAP processing allows automated data processing after each sample is analyzed (i.e., real-time processing)
  • Web-based results summary including color-coded sample browser viewable from any web-browser
  • Excel-based sample list import and results summary
  • XML output aides in capturing results for LIMS or database

Choice of Two Different HT Platforms!

 Oligo HTCS Vanquish system, featuring: the LTQ-XL   mass spectrometer and Vanquish dual pump UPLC
 Oligo HTCS DHR system, featuring: the LTQ-XL mass   spectrometer, UltiMate 3000 HPLC, and CTC PAL3   DHR autosampler

What’s Included with the Oligo HTCS

The Oligo HTCS includes everything you need to characterize your oligos using either high-throughput or detailed LC/MS methods. We install the system, provide detailed training for your users, and guarantee your success with the application. As part of the package, we provide ready-to-run methods for both high-throughput analysis and detailed LC/UV/MS profiling of oligos. Our standard Oligo HTCS package includes:

  • **New** Orbitrap Exploris MX HRMS LC/MS system from Thermo Scientific
  • Standard Oligo HTCS Vanquish system utilizes Vanquish UHPLC with dual pump, Flex autosampler, and UV detector from Thermo Scientific
  • Ultra-high throughput Oligo HTCS DHR system includes: 2 x UltiMate 3000 dual gradient pumps,  LEAP CTC PAL3 DHR autosampler, with 2 x high-pressure injector valve(s), 2 x wash systems, and your choice of 6×96 deep well or 12×96 shallow well sample cooling compartment
  • Novatia ProMass oligonucleotide data processing software package
  • Instrument methods for on-line desalting using dual trap column desalting platform for maximum throughput (2000 samples/24 hrs or >3000 samples/24 hrs for DHR system)
  • Instrument methods for detailed LC/MS profiling analysis
  • Oligo HTCS applications pack, includes a supply of analytical and desalting columns, buffer conditions, and method files
  • Installation, training, system documentation, and full application support including a one year warranty
  • Fully configurable to suit your analysis and budget requirements, including configurations for users with existing Thermo LC/MS systems

Who uses the Oligo HTCS?
Oligo HTCS systems are in use world wide in DNA/RNA manufacturing and pharmaceutical research environments. Some of our users include:

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