Expert FAQ: Transitioning to Hydrogen for GC and GC/MS Systems

by , | Jan 27, 2025

Learn how to switch to hydrogen carrier gas for GC and GC/MS, with expert insights on safety, system adjustments, and maintaining gas purity.

Hydrogen is gaining traction as a carrier gas for gas chromatography (GC) and GC-mass spectrometry (GC/MS), providing a cost-effective alternative to helium. But making the switch isn’t as simple as flipping a valve—method compatibility, safety concerns, and system adjustments all play a role.

In the latest Ask the Agilent Experts webinar, Vanessa Abercrombie (GC Applications Chemist, Agilent) and Ed Connor (Product Manager, PEAK Scientific Instruments) shared actionable tips for navigating this transition with confidence. Read on for key highlights, and register for the full session to explore their advice in detail.

Transitioning from Helium to Hydrogen: What You Need to Know

“Before even addressing the GC setup, check how the gases are connected,” says Abercrombie. She describes how copper tubing, although a standard choice in labs, isn’t recommended for hydrogen due to its reactivity and potential for leaks. Stainless steel is a safer alternative.

Abercrombie encourages the use of simulation tools, such as method translators, to predict how factors including flow rates and pressures could impact existing setups. For example, hydrogen’s unique properties can lead to negative head pressure when using helium-compatible flow rates, often requiring narrower columns to compensate.

Connor stresses the importance of verifying that both your GC and methods are compatible with hydrogen as a carrier gas, particularly for regulated methods where approval may be required. He observes that hydrogen demands about 25% more gas volume than helium, which should be accounted for when selecting the appropriate generator.

Maintaining Gas Purity: Tips for In-House Generation

When asked about common contaminants from gas generators, Connor identifies nitrogen, oxygen, and moisture as the primary culprits. “Nitrogen only appears if there are leaks in the supply lines or generator,” he remarks. “Check connections regularly, and remember that as hydrogen leaks out, air can be taken in.”

Connor explains that oxygen contamination without nitrogen—indicating it’s not caused by an air leak—may signal damage to the proton exchange membrane (PEM) cell, often requiring costly replacement. He advises using high-purity deionized water to protect the PEM cell and extend its lifespan.

Addressing moisture in hydrogen generators requires effective drying methods. Desiccant dryers, though common, require frequent replacement to maintain performance. Pressure swing adsorption (PSA) dryers use regenerable materials to remove moisture non-stop, keeping hydrogen dry without frequent shutdowns that risk air or other impurities entering the system.

Even the best hydrogen generator requires proper care to perform reliably, explains Abercrombie. She emphasizes the importance of maintaining water purity by periodically replacing the deionizer (DI) column. “If you’re not supplying clean water, performing routine maintenance, and checking for leaks between your generator and instrument, you’ll run into issues with your analysis,” she says. “Unsure about what to replace or when? That’s why having a service contract for your gas generators is so important.”

For nitrogen and zero-air generators, Connor underlines the importance of using clean, oil-free air supplies to prevent contamination. A catalytic (CAT) chamber can remove ambient methane, a key volatile organic compound (VOC), to stabilize baselines and improve gas quality. Regular maintenance, including annual filter replacements, is critical for consistent gas quality. 

Best Practices for Reducing Leaks in GC Gas Lines

Dealing with extremely light gases such as hydrogen means leaks are always a concern. Preventing them starts with understanding where they’re likely to occur—such as connection points—and how to spot GC leaks early.

“Use a leak detector to inspect gas lines, the back of your GC, and column connections inside the GC,” advises Abercrombie. “Any leaks at the column connections won’t just impact chromatography—they’ll also let oxygen into the column, which can damage the column phase.”

Both experts discuss the value of indicators for detecting and preventing leaks. They highlight color-indicating gas filters as key tools, explaining that top-down color changes suggest gas line issues, while bottom-up changes point to the GC. Filters purify carrier gas, reducing background noise and improving sensitivity, but Abercrombie reminds us that filters can't work miracles—you still need to start with the purest gas possible.

Connor recommends indicating gas traps for early leak detection, preventing column damage and GC contamination. He adds that gas traps last longer with generators, which produce cleaner gas than cylinders, making them a reliable and cost-effective option.

Connor also outlines practical steps to minimize leaks, such as properly tightening compression fittings, positioning ferrules correctly, and inspecting nuts for wear.

Ensuring Safety When Switching to Hydrogen Carrier Gas

Safety is often the first concern for customers exploring hydrogen as a carrier gas, notes Abercrombie. However, she explains that hydrogen’s diffusive nature makes it difficult to reach explosive concentrations, and most labs already use it safely at higher flow rates with flame ionization detectors (FIDs). For additional safety, she suggests installing hydrogen sensor modules or exhaust vents near GC/MS systems.

Chemical reactivity is another factor to consider. Abercrombie encourages steering clear of chlorinated solvents whenever possible. If unavoidable, she recommends using a Multi-Mode Inlet (MMI) and starting with lower inlet temperatures to reduce the risk of hydrochloric acid formation. For mass spectrometers, coated ion sources such as the HydroInert Source minimize spectral tilting—data distortions caused by hydrogen—ensuring more accurate compound identification.

Abercrombie highlights that hydrogen’s natural scrubbing action offers significant benefits for mass spectrometer care, keeping the ion source cleaner for longer and reducing upkeep needs. She adds that Agilent’s JetClean self-cleaning ion source technology has demonstrated how hydrogen improves system performance over time.

This scrubbing effect can also dislodge deposits in gas lines, exposing buildup when transitioning from helium. “That’s why we recommend replacing your gas lines at the same time as you switch carrier gas,” says Abercrombie, noting the importance of addressing these changes to stabilize baselines and reduce background noise.

“Using a hydrogen gas generator is the safest way you can produce hydrogen in the lab,” states Connor, citing their low gas volume storage, reduced operating pressures, and integrated safety features when compared to cylinders. He adds that generators can support multiple GCs efficiently, supplying both carrier and flame gas, and that in-oven leak detectors can automatically stop gas flow if a leak is detected.

Air Contamination Risks in GC and GC/MS

A webinar attendee asked whether air can enter gas lines through a leak, even in a pressurized system. Both experts confirmed this is possible and emphasized prevention steps.

“Any leak in your gas line will let air and other contaminants in,” explains Abercrombie. She advises rigorous leak checks from the generator to the instrument and stresses that environmental factors, such as temperature and humidity near the generator, can also cause issues. Routine maintenance and service contracts are key to maintaining reliability.

Connor adds that leaks at joints or fittings can draw air into gas lines, introducing oxygen and moisture that compromise results. He warns that nitrogen leaks, while less discussed, can displace oxygen, creating a hazard. “This is another reason why a gas generator is a safer option than bulk supply,” he notes, “since the generator will not change the lab atmosphere as nitrogen cylinders or dewars might.”

Hydrogen’s Real Potential

Hydrogen provides a safe, efficient, and reliable alternative to helium when supported by proper systems and safeguards. It offers financial stability, reduces reliance on external markets, and supports sustainability without compromising performance. Explore strategies for adopting hydrogen carrier gas in 'Ask the Agilent Experts Series – Part 6: The Gas Edition.' Register today to hear Abercrombie and Connor tackle user-submitted challenges with practical, real-world solutions.


About the Experts

Vanessa Abercrombie
MFS, GC Applications Chemist, Agilent Technologies

Vanessa Abercrombie is a GC applications chemist at Agilent Technologies in Folsom, California, USA. Vanessa has a broad background in GC and GC/MS, including experience as an instrument chemist at Bode Technology in Virginia working under contract to the FBI’s Laboratory Division. Prior to that, Vanessa worked for ETS Labs in St. Helena, California, as an analytical chemist, where she researched and developed quantitative separations by GC/MS and UHPLC for beer, wine, and spirits. She holds a Masters of Forensic Science from The George Washington University and a Bachelor of Arts in Chemistry from Sonoma State University.

Ed Connor
Product Manager, PEAK Scientific Instruments

Ed joined PEAK in 2013 as a GC product specialist and then moved to product management. He’s been working on many collaborative projects with PEAK customers and major instrument manufacturers worldwide. The main focus of these collaborations has been looking at conversion from helium to hydrogen carrier gas for GC applications. Ed completed his Dr.Sc. at ETH Zurich in 2007 using GC-MS to look at herbivore-induced plant volatiles and their interaction with beneficial insects. He then joined the University of Zurich where his work focused primarily on floral volatile analysis using a variety of volatile collection methods, GC-MS, and GC-FID.

Sponsor:

Watch on demand:

Related Content