Ongoing Care and Feeding of Your Gas Chromatograph: Preventing Problems Before They Start

Troubleshooting in gas chromatography has become much simpler over the years, with modern systems often having automated diagnostics that help ensure proper operation. However, not all troubleshooting and preventive maintenance can be performed using these diagnostics; often they only assist in identifying a problem, not solving it. Fortunately, many of the instrument and supply vendors have provided simple guidebooks and materials for troubleshooting and maintenance. An example article from LCGC is referenced here; check with your instrument or column vendor for their own guidebook, poster, or website.¹ ChromAcademy, LCGC International’s online training system, includes many modules and tutorials relating to troubleshooting and maintenance.² Many of the problems discussed in these guides can be avoided or mitigated with some simple preventive maintenance and care for the instrumentation and consumables. Proactive troubleshooting and prevention are ongoing topics; see some previous columns for more details.^3-5

Capillary GC Is Clean GC

A gas chromatograph is among the most versatile, rugged, and straightforward analytical instruments to operate. However, like your car or yard equipment, it requires periodic care and maintenance to maintain smooth and proper operation. Many gas chromatographs that were built decades ago are still operating (usually with newer data systems–a topic for another article) because of regular and purposeful ongoing care and maintenance.

The most important principle to remember for both maintenance and quantitative performance was taught to me early in my career in an ACS Short Course, “Capillary GC is Clean GC.” Always be thinking about cleanliness and preventing contamination of the instrument, its laboratory environment, connections, supplies, and samples. Think about the column and stationary phase; a typical capillary column has only a few milligrams of stationary phase in the entire column. It is easy to imagine that far smaller quantities of contaminants can impact separation performance.

We will now explore some of the critical areas of the gas chromatograph that are easily overlooked but can have major impacts on instrument performance if not maintained regularly. These include carrier and detector gases and scrubbers, inlet parts and consumables, and column and detector care.

Keep the GC up and running. The single step that can be taken to ensure the best performance is to keep the system up and running all the time. Most newer systems have a sleep or power- and gas-saving mode that slows down the gas flows, especially for the expensive helium, but keeps the system itself up and running with the inlet, column oven, and detector zones heated. It is especially important to keep the inlet and detector hot to prevent laboratory contaminants from condensing on or in them. The column oven can be kept at a suitable lower temperature, usually the starting temperature of a typical method or run.

Clean GC begins with clean gases. All the gas supplies, carrier gas, detector, and makeup must be scrupulously clean or various instrumental, column, and performance problems can result. While many laboratories use high-purity gas generators for gases such as hydrogen, air, and nitrogen, we all still obtain helium in cylinders. If possible, I recommend changing from helium to nitrogen, which is much less expensive, more sustainable, and easily generated in very high purity.^4,5 Here’s a quick trivia question: How often do you think a gas cylinder is cleaned at the factory? (Answer is at the end of this paragraph.) When returned to the factory, cylinders are connected to a huge gas manifold, refilled and shipped to the next user. Over time, contaminants can accumulate in the cylinder and accumulate at the bottom of the tank. Think about liquid propane tanks under high pressure; substances that are gases at atmospheric pressure can liquefy and sink to the bottom of the tank. As the gas is used, the liquified contaminant eventually expands and contaminates the gas more as the cylinder is expended. Never let your cylinders “run dry.” Replace the cylinder when the gauge pressure reaches 100 psi (about 700 kPa). Answer to the trivia question: Once, when it was made.

Check or replace your gas scrubbers often. Whether using cylinders or generators, all gas systems include scrubbers or filters needed to remove contaminants. If using gas generators, of course you should follow the manufacturer’s instructions for ensuring proper gas purity. If using cylinders, you may have one or more sorbent-based traps located on your gas lines between the gas tank and the instrument. At a minimum, scrubbers that remove oxygen and water should be used. Depending on the application, additional scrubbers may be needed. They should be replaced on a schedule, or if indicating scrubber materials are used, replaced when indicated. Scrubber replacement is often included as part of periodic maintenance in service contracts. This is easy to ignore. The only thing worse than a dirty scrubber is an overloaded one. Once the scrubber is overloaded, contaminants can enter the carrier gas flow, resulting in elevated baselines, increased noise, ghost peaks, or in the extreme, column degradation.

Many problems can be traced to a dirty inlet or samples. The inlet and injection process are often the most complex and confusing aspects of a gas chromatographic method. A scan of the various troubleshooting guides referenced in this article shows that about 70 percent of problems in gas chromatography, especially relating to losses in separation or quantitative performance, are inlet-related. The inlet is the critical space where the sample is injected, heated, vaporized, mixed with carrier gas, and transferred to the column. There are myriad choices and settings, each of which can affect performance. These are discussed in more detail for splitless inlets in several previous installments.⁶ If you are experiencing peak tailing, other poor peak shape, or loss of reproducibility that has become worse over time, it is likely inlet contamination; change the septum and glass liner.

Change septa and inlet liners often and use the correct septum and inlet liner for your application. Split and splitless inlets have two weak points that are readily subject to contamination: the septum and the glass inlet liner. Polymeric septa are used to allow the syringe to enter the inlet and inject the sample without breaking the seal and leaking. Depending on the specific syringe and needle type, septa have a very limited lifetime, typically 30 to 50 injections. For capillary gas chromatography, make sure to use high-temperature septa formulated for capillary columns. When changing the septum, make sure that the septum nut is not tightened too tightly (firm finger tightening should work) and that you note the change in the logbook or reset the injection counter in the data system.

Not all glass liners are alike. If you have ever shopped for glass inlet liners for split and splitless inlets, you see that there are myriad choices and configurations. Make sure you are using the correct inlet liner for your application. A well-written method should specify the exact liner to use. An incorrect liner is one of the most common causes of poor quantitation. Whenever the liner is changed, this must be noted in the logbook or recorded in the data system. The glass liners for split and splitless injections are very different and perform different functions. The split liner has a larger internal volume to accommodate rapid sample and solvent vaporization, while the splitless liner usually has a smaller volume to accommodate slower solvent vaporization. The injection process is so complex that books have been written about it, and it is still not fully understood.⁷

Capillary columns are delicate; handle and treat them with care. First and foremost, always have carrier gas flowing through the column; avoid letting in air and water. For most of our stationary phases, remember that there are only a few milligrams of stationary phase in the whole column, and that they are manufactured from very high-purity polydimethylsiloxane, which is highly inert. Carrier gases helium and nitrogen provide among the most inert environments available; the inside of a capillary column with carrier gas flowing is one of the most inert places in the field of chemistry. Our job is to keep it that way. As a capillary column ages, contaminants can build up at the column head near the inlet. Eventually, this can result in poor peak shape (usually tailing) for more polar or reactive analytes.

Keep your detector heated and running. Most detectors are heated for one reason: keeping it clean. It should always be maintained at operating temperature, except when undergoing repair or maintenance. If left cooled for extended periods, contaminants from the laboratory can condense or adsorb on detector surfaces, resulting in elevated signals and/or noise, resulting in loss of quantitative performance.

Check the baseline. One simple way to monitor detector operation daily is to check the baseline. With the system ready to run, or by running a short (one minute or so) blank run, with no injection, record the blank run, which should show only the baseline. Examine the chromatogram by magnifying the plot until the random baseline noise fills most of the screen. Today’s baseline should look the same as yesterday’s. The amplitude, distance from the lowest spike to the highest one, should be the same and the background signal itself should be the same. If either has elevated, something that should be addressed has happened. An elevated but smooth baseline can result from dirty carrier or detector gases (Was the tank just changed? How would you know if the tank was changed?) Whatever the contaminant is, it is continuous. An increased noise amplitude has several causes, but commonly can result from the electronic environment. Are there any other instruments or devices on the same circuit? Each instrument should be on its own circuit.

Keep detailed records or logs of maintenance activities. Many of the newer instruments can track this for you if the capability is activated in the data system; most older systems do not. If the system does not track maintenance, an old-fashioned logbook can still be used and is often more effective when quick retrieval of maintenance information or notes is desired. As we have discussed, consumables such as septa, inlet liners, and columns have limited lifetimes, usually based on the number of samples run. Whenever one of these is changed, the sample counter, either in the data system or a logbook, should be reset.

To prevent small problems from becoming big ones, troubleshooting and preventive maintenance are an ongoing task. Check the gas flow, syringe, injection count on the septum, and detector baseline daily. Watch your chromatograms and do not just count on calculations such as tailing factors being in a normal range. Look at the chromatograms; if tailing is starting to appear but is still within specification, it is still an indicator of upcoming problems and should be addressed. Keep detailed records of all maintenance activities, changes in consumables, and any time you turn a wrench. These will be valuable in the event that more extensive repair, or a service call, is needed. As discussed in my early column,³ a gas chromatograph can provide decades of service if well cared for and fed.

References

1. Watson, D. W. GC Troubleshooting in Simple Pictures, Part I. LCGC North Am. 2016, 34 (10), 818.
2. CHROMacademy. Accessed February 16, 2026. https://www.chromacademy.com/
3. Snow N. H. Stopping GC and GC–MS Problems Before They Start. LCGC North Am. 2019, 37 (1), 18-23.
4. Bulsiewicz, A.; Mizvesky, J.; Snow, N. H. How Green is your Method? Evaluating the Sustainability of Analytical Methods. LCGC International 2025, 2 (9), 8-12. DOI: 10.56530/lcgc.int.lb7480q2
5. Snow, N. H.; McCann, S. P.; Handzo, B. et al. Go With the Flow: Thinking About Carrier Gas Flow in GC. LCGC North Am. 2020, 38 (3), 152-158.
6. Snow N. H. Optimizing Splitless Injections in Gas Chromatography, Part III: Setting Up and Optimizing the Inlet. LCGC International 2025, 2 (2), 16-19. DOI: 10.56530/lcgc.int.rs5970s7
7. Grob K. Split and Splitless Injection for Quantitative Gas Chromatography: Concepts, Processes, Practical Guidelines, Sources of Error; 4th, Completely Revised Ed: John Wiley and Sons, 2007.