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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 Ultimate is truly a unique system for oligonucleotide analysis. The system will analyze 1500 samples/24 hrs in high-throughput mode, but has the flexibility to be automatically switched from high-throughput to detailed LC/MS profiling mode from within a sample list run. The HTCS is also fully upgradeable to our HTCS Twin system when you need more throughput.
  • The Oligo HTCS Twin Ultimate is designed for those who need the highest possible throughput and highest quality in oligonucleotide mass analysis. The Twin system employs a dual-arm autosampler to achieve a 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
  • Automated analysis includes built-in desalting for each oligo analyzed
  • Analysis throughput 1500 samples/24 hrs (3000 samples/24 hrs with Twin 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 UltiMate System Oligo HTCS UltiMate system, featuring: the LTQ-XL mass spectrometer, Vanquish or UltiMate 3000 HPLC, and HTC-PAL-xt autosampler
Oligo HTCS Twin UltiMate System Oligo HTCS Twin UltiMate system, featuring: the LTQ-XL mass spectrometer, UltiMate 3000 HPLC, and Twin HTS-PAL-xt 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:

  • LTQ-XL LC/MS system from Thermo Scientific
  • Vanquish UHPLC or Ultimate 3000 HPLC system with dual gradient pump(s) and UV detector from Thermo Scientific
  • LEAP CTC single or Twin PAL-xt autosampler, with high-pressure injector valve(s), DLW wash system(s), and your choice of 6×96 deep well or 12×96 shallow well sample cooling compartment(s) standard
  • Novatia ProMass oligonucleotide data processing software package
  • Instrument methods for on-line desalting using dual trap column desalting platform for maximum throughput (1500 samples/24 hrs or >3000 samples/24 hrs for Twin 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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