Helium has long served as the default carrier gas in gas chromatography (GC) and GC–mass spectrometry (GC–MS). That standard now faces pressure. Supply constraints, rising costs, and sustainability concerns have pushed laboratories to evaluate alternatives.
This article draws on insights shared in the webinar “Helium Shortage 4.0: Is Hydrogen Carrier Gas the Solution to the GC–MS Problem?”, hosted by Separation Science in collaboration with Markes International. The session features a panel of experts, including Diane Turner (Director & Senior Consultant, Anthias Consulting Ltd), Chris Siegler (R&D, Dow Inc.), and Helen Martin (Thermal Desorption Business Unit Manager, Markes International), moderated by Matthew Klee (President, XO Associates LLC). Together, they examine the impact of helium shortages on GC–MS workflows and assess whether hydrogen can serve as a practical, high-performance alternative.
Why Helium Is Losing Ground
Helium’s limitations drive the conversation. It is a finite resource, sourced as a byproduct of natural gas extraction. Supply disruptions over the past decade exposed its vulnerability, creating price volatility and availability issues.
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“Helium availability continues to fluctuate, and many laboratories now struggle to secure a reliable supply at a predictable cost,” explains Martin.
Labs that rely heavily on GC workflows face real operational risk. Instrument downtime, delayed analyses, and rising consumable costs all trace back to dependence on helium. These pressures have turned alternative gases from optional to essential.
Evaluating Alternative Carrier Gases
The session focuses on two viable replacements: hydrogen and nitrogen. Each presents trade-offs that labs must weigh against their application needs.
Hydrogen stands out for performance. It enables faster linear velocities, which translates to shorter run times and higher throughput. It also supports efficient separations without sacrificing resolution when methods are optimized correctly.
Nitrogen offers a different profile. “While nitrogen is an option, it doesn't offer the faster chromatography we see with helium or hydrogen, which limits its appeal for high-throughput workflows,” Martin points out. However, Siegler notes it can still serve a valuable role in the lab as a makeup gas for flame ionization detectors (FID) or for switching valves, helping to conserve helium where it is strictly required.
A key topic discussed in the webinar centers on thermal desorption (TD) workflows. Historically, older systems were less flexible, but instrument vendors have introduced multi-gas-capable systems.
“With newer multi-gas platforms, analysts can start to evaluate hydrogen in applications where it simply wasn’t an option before,” Martin notes.
When migrating TD workflows to hydrogen, understanding the instrument's chemical interactions is critical.
“You have to think about the temperatures your compounds are being exposed to while in that hydrogen carrier gas, from the focusing trap through the heated transfer line,” explains Turner. “Minimizing activity and reducing temperatures where possible is key to preventing unwanted catalytic degradation or hydrogenation reactions.”
The takeaway is direct:
- Hydrogen suits labs that need speed and scalability
- Nitrogen is highly stable but slower, often best utilized as a makeup or purge gas
- Helium remains viable but no longer essential
The decision hinges on throughput demands, method constraints, and instrument compatibility.
Safety Considerations Shape Adoption
Hydrogen’s flammability often raises concern. The webinar addresses this directly: modern systems mitigate risk effectively when configured and maintained properly.
“With modern hydrogen generators and appropriate safeguards, the risks are well controlled and comparable to other gases used in the lab,” Martin emphasizes.
From a user perspective, Turner highlights the perception gap. “There is still hesitation around hydrogen, but much of that comes from outdated assumptions. In reality, the way we generate and use hydrogen today is very different from traditional cylinder-based approaches.”
Hydrogen generators play a central role. They produce gas on demand at low volumes, reducing the hazards associated with high-pressure cylinders. Integrated safety features—leak detection, automatic shutdown, and inline excess flow limiters—further limit exposure.
Siegler adds a practical perspective. “If you approach hydrogen with the same discipline you apply to any laboratory gas system—proper installation, monitoring, and maintenance—it becomes a manageable part of the workflow.”
Converting GC and GC–MS Systems
Switching carrier gases requires more than a simple swap. Method parameters must adapt to the physical properties of the new gas.
“You cannot simply replace helium with hydrogen and expect identical results—you need to adjust the method to match the gas properties,” Turner explains.
Key areas of adjustment include:
- Flow rates and linear velocity
- Oven temperature programs
- Column selection and dimensions
- Mass spectrometer vacuum system capacity
GC–MS systems require additional attention. Vacuum conditions are particularly critical because hydrogen is a lighter gas and behaves differently from helium under vacuum.
“You have to ensure your mass spec’s vacuum system can actually work efficiently at the higher optimal flow rates required for hydrogen. If your turbo pump can’t cope, you’re going to lose the sensitivity you were trying to gain,” Turner notes.
For labs that cannot immediately switch to hydrogen due to regulatory or method constraints, conservation is the best interim strategy.
Siegler advises running a routine "helium mass balance" across the lab to identify hidden leaks and track actual usage. “Implementing features like gas saver mode to lower split vent flows during a run, and making sure to turn off auto-prep run when the instrument is sitting idle, can save a massive amount of helium,” he explains.
Application Impact: What Labs Can Expect
Real-world examples presented in the webinar highlight measurable gains, particularly for industrial and manufacturing applications.
In production environments, such as chemical plant labs, maintaining quality measurements and avoiding downtime is critical to shipping product. Hydrogen can significantly reduce analysis time while maintaining resolution, protecting the lab from supply chain disruptions.
“We've actually taken a 23-minute long run using helium and been able to get it down under 14 minutes while keeping everything similarly separated,” Siegler asserts.
However, the benefits come with additional considerations. Labs must account for method redevelopment and validation—especially in regulated industries.
“If you are working in a regulated environment, switching carrier gas is not just a technical change—it triggers revalidation,” explains Siegler. “That can be a significant barrier depending on your workload and compliance requirements.”
In some cases, sensitivity improves due to sharper peak shapes and reduced diffusion effects. However, this is method-dependent and requires optimization.
The impact is clear: hydrogen offers strong performance advantages, but the benefits depend on application, instrumentation, and the resources available for method redevelopment.
Strategic Implications for Laboratories
The shift away from helium reflects a broader trend: labs are building resilience into their workflows. Carrier gas selection now intersects with cost control, sustainability, and operational continuity.
Hydrogen leads this transition. It offers a practical path to reduce dependency on a constrained resource while improving performance metrics.
Labs that delay adoption risk higher costs and reduced flexibility. Those who act gain control over supply, throughput, and long-term planning.
Helium will not disappear overnight. But its dominance has already started to erode. The question is no longer whether alternatives work—it is how quickly labs can implement them without disrupting results.
Watch the full webinar: For deeper technical insights, detailed discussion, and audience Q&A, view the on-demand session.
