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Choosing the Right LC-MS System

Panelists from Our February 23 Webinar Identify Key Features to Consider When Purchasing an LC-MS System

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In March 2011, Lab Manager organized a “Product Showcase” webinar focused on the new features and applications of LC-MS systems, which are analytical systems involving liquid chromatography (LC) separation coupled with mass spectrometry (MS)-based detection. The webinar featured a panel of four experts representing some of the leading vendors in the field, who provided their perspectives on the trends in the LC-MS market and what users should consider when deciding which LC-MS is right for their lab based on their samples and applications. Once again, this online event attracted a large international audience from diverse industries who were looking for an opportunity to interact with the panelists in real time and get their advice on the key factors they should consider when making their buying decisions. Each panelist gave a brief presentation to outline the latest in LC-MS systems and to help users decide which one is right for them. Webinar participants included:

  • Hayley Crowe, Mass Spectrometry Detection Specialist, PerkinElmer
  • Diab Elmashni, Senior Marketing Manager for LC and LC/ MS, Thermo Fisher Scientific
  • Robert Classon, LC-MS Business Development Manager, Shimadzu Scientific Instruments
  • Frank Steiner, Ph.D., Manager for Small Molecule Solutions, Dionex Corporation
  • Moderator: Tanuja Koppal, Ph.D.

Below are answers provided by the panelists to attendees’ follow-up questions.

Q: If you already own an LC-MS system, when do you know it’s time to upgrade? What are some of the advantages of transitioning to a UHPLC-MS?

Crowe: The UHPLC technology has proved to be a powerful approach for improving chromatographic analysis in terms of throughput and resolving power. When it is coupled with MS, users are getting more information, better response time for process monitoring and product release, and ultimately more samples analyzed per day.

Elmashni: It is time to upgrade your LC-MS when its level of performance is no longer suitable for your needs or when it is too slow to keep up with newer technology such as the speed of UHPLC. Also, as MS instruments age, if they are not refurbished, they tend to lose sensitivity as the internal components age. The advantages of transitioning to UHPLC-MS are that it provides the user with a much higher throughput, lower solvent costs, and shorter method development times. UHPLC also provides better separation than traditional HPLC.

Classon: The choice should be application-driven. If your old instrument isn’t sensitive enough to detect or quantitate at the levels you want, then you should consider an upgrade. However, do not assume that a more sensitive instrument will be suitable for all applications. Quite often the problem is sample prep or chemistry-related. But if you need faster speed to improve productivity or throughput, then consider the LC-MS instruments that have been introduced in the past year. There has been a considerable increase in speed in many of the more recent instruments.

Steiner: Mass spectrometers for LC have made significant progress in sensitivity and speed, and also have improved in mass resolution and accuracy. At the same time, electrospray sources have been optimized for higher sensitivity even at increased flow rates. High scan speed to achieve data rates of more than 20 Hz are crucial in order to benefit from the throughput potential of UHPLC on short- and medium-length columns. If the typical 2.1 mm internal diameter (id) columns are to be used at highest speed, the MS should support flow rates of 1 to 2 mL/ min without significant loss in sensitivity. A transition to LC-MS with an appropriate instrument and software combination can significantly boost lab productivity and data quality, thus increasing value in all markets.

Q: What are some of the key challenges around sample prep, carryover, and cleanup for LC-MS and how can you minimize those problems?

Crowe: A significant breakthrough in LC-MS functionality is the snap-in probe design. The probes can be specific to a user, application, or sample type, helping to minimize the risk of carryover, cross-contamination, and instrument downtime.

Elmashni: Samples injected into an MS detector must be cleaner and smaller in quantity than those injected in a UV detector. Carryover becomes extremely important when you add an MS detector, because the level of sensitivity is so high that it can easily see carryover that would not be seen in a UV detector. Carryover can make your sample appear larger than it really is, thereby giving you false results. An MS detector requires cleanup in the source and the source housing because the sample is sprayed at the analyzer. If they are not cleaned regularly, it will cause carryover.

Classon: With UHPLC chromatography columns, the frits and packing can clog easily. So sample cleanup, especially how you remove proteins from biological matrices, becomes quite important. Faster chromatography also means a greater probability of having co-eluting components that could affect ionization and make quantitation more variable. Solvents too may require filtration to get longer life out of the pump seals.

Steiner: LC-MS does not normally require different sample prep or cleanup than other LC techniques for accurate short-term results. Long-term signal stability of ion sources generally improves with matrix removal, although good progress on auto-clean options has been made on the MS side. The UHPLC part can be more demanding as small particle columns with finer-mesh retainers clog more easily. Small-volume, high-resolution columns are less forgiving of solvent mismatch (if sample solvent elutes stronger than mobile phase). This can be addressed by smaller injection volumes, but at higher detection limits. Smallest sample carryover is a key metric but must be assessed based on identical compounds and injection/ needle wash procedures.

Q: What are some of the key factors that need to be considered when choosing the right software for data analysis and data integration?

Crowe: Modern LC-MS instrumentation generates a lot of data very quickly. Being sure the reported results are correct is critical to any analytical laboratory. Things like homogenized data treatment, high accuracy of data processing and result analysis, and high-throughput review of results are paramount for productivity and ease of use.

Elmashni: With MS detection, every vendor controls only their own instrumentation. This is not the case with HPLC/UHPLC, mainly because the software control for MS detectors is very labor intensive and has proprietary information that assists in the performance of the MS detector. Ideally, you would look at the different features with respect to ease of use, standard data reporting templates, and customized software options for your specific application and choose the one that works best for you.

Classon: Pick the software that is easy to use and protects the instruments from doing things that might lead to contamination or clogging. Most instrument software will check to make sure you have liquid flow and gas flow before making injections, or will start up or shut down properly in the event of a power outage. Although such events might not occur often, it is very worthwhile to have the software protect everything from even a temporary power interruption.

Steiner: This depends on what the focus is. MS software packages provide good tools for de-convolution on the mass axis and support all the tandem MS features, but are usually not as good to assess peak shape and separation quality parameters on the time axis, which is crucial for the chromatographer. Accurate peak integration for quantitation is usually better supported in LC software, and this recently underwent significant improvement in some chromatography data systems. Ideally, the user should be free to choose his hardware-software combination and be able to use the best of both worlds to his advantage.

Q: How important should factors like technical service and warranties, user training, and availability of supplies and accessories be in your decision making, and what’s the best way to get information about them up front?

Crowe: In today’s challenging environment, having a complete solution is critical for the laboratory’s performance. Ease of use, cost of operation, and cost of maintenance of the equipment can sometimes be even more important than the pure instrument performance, especially in a QA/QC environment.

Elmashni: These items are extremely important when choosing an MS vendor. MS detectors cannot be serviced by the user, so it is very important to have a vendor with a fast-responding and competent service organization. The same goes for user training. These are very difficult instruments to learn how to use, and the user training is vital to becoming efficient on the instrument. Supplies and accessories are important because a vendor who has all the items provides the customer with time savings, better negotiating power for discounts, and the certainty of getting the specific parts for that instrument.

Classon: I recommend getting to know your local service person/manager. Warranties are nice, and training can be helpful, but when something needs repair or adjustment, it is the people that matter. A lot of companies have tried singlevendor repairs for all products and some have been disappointed with the reliability of repairs or the non-factory parts that have been utilized. Stick with people you can trust.

Steiner: The more technically advanced the analytical instrument, the more crucial these criteria are. While modern instrument development increasingly focuses on robustness, usability, and serviceability, this still provides an intrinsic challenge both on the LC and the MS side. Hence, a critical comparison of the complete package is mandatory. The best way to get information is to speak to the vendor’s customer base, e.g., at conferences and user meetings, but ideally speak to people who you can trust. Opinions in forums can sometimes be misleading as one never knows exactly how the information was introduced there. Social media are another emerging source of information.

Q: In what areas of LC-MS can users expect to see most changes and improvements in the near future?

Crowe: Chromatography might become less critical is some quality control assays. The advent of direct sampling analysis for MS ion sources is providing the opportunity to minimize sample prep or to deal directly with samples with no preparation at all. This allows one to run many samples/hour and eliminate artifacts.

Classon: Improvements in sensitivity will continue, but we are getting close to the practical limit now. We may see some greater convenience features in new models and improvements in speed and mass accuracy. I expect to see more development of ambient ionization sources, increased use of ion mobility technologies in the high pressure/ambient regions of the instrument, and perhaps some overall size and cost reductions.

Elmashni: Software is going to be the next major development area. As more laboratories employ technicians to run standard testing, the software of the instrumentation has to be conducive to that environment by making the detectors easier to use and maintain.

Steiner: The current technical progress will not slow down, and we will see further improvement in specifications on both the LC and MS fronts. Hopefully there will be more new LC columns with low bleed that allow benefits from improved LC instrument specifications. A strong focus of the development will certainly be on ease of use and instrument uptime. Both will be enhanced through development on the hardware side, but even more important on the software side, where the worlds of LC and MS are yet far from being fully integrated. Further improved integration of method development and sample prep into the automated instrument workflow is another driver for development in the near future.

To view the archived webinar, please visit The website also hosts a number of LC-MS systems-related articles, application notes, and information on upcoming events and webinars.