Skip to main content

Oligo HTCS Frequently Asked Questions

  • How do I know the system will work for me? We use the same system in our lab as part of our fee-for-service oligo analysis business. We know it works because we use it ourselves. As we like to say…”we eat our own cooking”.
  • What does H-T-C-S mean? HTCS stands for high-throughput characterization system.
  • Why do I need LC/MS or the Oligo HTCS, shouldn’t I just use MALDI-ToF? If you just need to run 20-mers, both the Oligo HTCS and MALDI-ToF would be comparable in performance. However, if you need to run oligos longer than ~40 bases, the Oligo HTCS is clearly superior. Also, the Oligo HTCS allows for intact analysis of DMT-on oligos and other oligos with labile groups not amenable to MALDI-ToF detection. Check out our presentation at ASMS where we performed a detailed comparison of the Oligo HTCS vs. MALDI-ToF for a wide range of oligos.
  • What does it cost (per sample) to operate the Oligo HTCS? The cost of running an Oligo HTCS in high-throughput mode is surprisingly inexpensive. In fact, our customers are telling us that our system costs much less to operate (per sample) than a popular chip-based MALDI-ToF system. The reason is that our system does not require you to purchase proprietary (expensive) consumables. This means that the Oligo HTCS will easily pay for itself over time, while giving you superior data quality for all of your oligonucleotide samples. Contact us to obtain a spreadsheet showing an example cost/sample breakdown.
  • I already have a Thermo LCQ or LTQ Series instrument. Can your HTCS be configured on my instrument? Yes. All components of our system are integrated with the Xcalibur data system and therefore will work with any Thermo Xcalibur-based system. We have many systems in the field using the LCQ and LTQ linear ion traps from Thermo.
  • What kind of instrument senstivity can I expect? For an ion trap instrument, we would typically inject 50-100 pmoles of oligo to get a high quality mass confirmation. The ultimate detection limit is in the femtomole range for full scan mass confirmation. During installation, we will demonstrate the successful analysis of 10 pmoles (1 uM x 10 uL) of a 20-mer oligo with 1 Da mass accuracy. Sensitivity for the LTQ series is considerably higher than the LCQ series instruments. We can routinely inject ten-fold less sample on the LTQ when compared to the LCQ.
  • My oligos contain salt, will I have to desalt them first? No! One of the great things about the Oligo HTCS platform is that desalting is an integral part of the sample injection process. Every oligo is desalted before it enters the MS ion source. This improves sensitivity and data quality in dramatic fashion. Integrated desalting also reduces the need for MS system cleaning and maintenance. We routinely analyze crude, ion exchange-purified, or PAGE-purified oligos with the system.
  • What is the typical mass accuracy? Mass accuracy is in the range of 0.01-0.02% over the course of a run. Unlike MALDI-ToF, mass accuracy and resolution is maintained even for the larger oligos.
  • How often do you need to mass calibrate the instrument? We have found that mass drift is largely a function of the laboratory temperature. If you have a stable lab environment, the mass calibration can last for months, while still providing a mass accuracy of 0.01-0.02%.
  • Is a warranty provided? Yes, each hardware component is covered under warranty from the original manufacturer.
  • How do you handle technical support and service? Since Novatia is running the Oligo HTCS in our own laboratory, it’s easy for us to answer your technical questions. If you are having an instrument problem we can remotely access your system via Webex for troubleshooting purposes. Most problems are resolved quickly over the phone. However, if a service visit is required, we are available to get you back up and running ASAP.
  • Can I send you some test samples? Indeed, we would be happy to run some samples for you to demonstrate the outstanding performance of the system. We would also welcome you to visit our lab to check it out for yourself.

If you have any additional questions or wish to inquire about our Oligo HTCS, email