Switching from Helium as a Carrier Gas: Can You Afford Not To?

Helium is a non-renewable element formed over billions of years via radioactive decay of Uranium 238, primarily extracted as a byproduct of natural gas via cryogenic distillation. It is indispensable across several sectors, with applications in magnetic resonance imaging (MRI) and nuclear magnetic resonance (NMR) cooling, as well as lifting gas (balloons and blimps), semiconductors, space applications, welding, and gas chromatography (GC), with chromatographic and spectroscopic uses accounting for approximately 15% of global usage (1). Despite global helium reserves estimated at 31.3 billion m³ (2)—enough for over 180 years at current usage (3)—frequent localized shortages persist, driven not by immediate scarcity but by production issues and geopolitical instability.

Major reserves are located in the USA, Qatar, Algeria, and Russia, with emerging high-grade deposits in Tanzania. The US Federal Helium Reserve, once a strategic stockpile, began phasing out federal (and hence price) control in 1996 and ended involvement in 2021, shifting supply responsibility to private industry, leading to market volatility. Geopolitical tensions have further strained the supply chain: Qatar’s 2017 blockade disrupted exports, and Russia temporarily embargoed helium for domestic use. Delays in launching new production facilities in Russia and Algeria have compounded uncertainty.

With helium demand projected to grow at a compound annual growth rate of 6.7% (4) and prices continuing to rise, laboratories face an unreliable supply future. Consequently, many laboratories have considered hydrogen or nitrogen as alternative carrier gases, balancing cost, performance, and safety in a volatile global helium landscape. Whilst vendors have focused efforts on developing equipment compatible with the use of alternative carrier gases, especially hydrogen, we estimate that fewer than 3% (based on our UK client base) of all GC–mass spectrometry (MS) instruments and applications have been converted to alternative carrier gases.

Why is there Reluctance to Switch?

Why indeed. It’s been three years since the last supply chain “crisis” and accompanying price hikes, and perhaps the imperative just isn’t there when compared to the effort required to switch to an alternative.

While safety concerns about using hydrogen as a GC carrier gas are often cited, modern chromatography systems and gas generators—with minor procedural adaptations—can effectively mitigate these risks. Safety may not be the primary barrier to switching from helium to alternatives such as hydrogen or nitrogen. Perhaps more significant obstacles include the initial capital investment required for gas generators or the lack of knowledge or expertise to successfully make the change. Less experienced users may be particularly reluctant to switch due to uncertainty around method translation, which is required to maintain separation performance when changing gases. Moreover, using hydrogen in GC–MS introduces added complexity, including potential reactions in the ion source and reduced spectral match quality with popular MS libraries such as the National Institute of Science and Technology (NIST). Perhaps practical, technical, and psychological factors—rather than safety alone—are key contributors to the slow adoption of alternative carrier gases.

However, the wider advantages of using an alternative carrier gas should not be overlooked. Aside from future proofing your gas chromatography supply base and ensuring price stability, hydrogen is fundamentally more efficient than helium, resulting in narrower peaks and the ability to produce higher quality separations or equivalent separation in significantly shorter run times. Both hydrogen and nitrogen can be produced easily in the laboratory and do not deplete a finite natural resource, supporting the move toward more sustainable practices. For less complex separations, nitrogen can be highly economical and result in very effective separations at lower carrier gas flow rates.

The factors required to switch to an alternative carrier gas are worthy of further consideration, with a view to helping the reader assess the possibility or necessity to make the change.

Alternative Carrier Gases and Hydrogen Safety Concerns

Conversations regarding the change to hydrogen as an alternative carrier gas often begin with questions or concerns regarding the use and storage of hydrogen within the laboratory. We first wrote about the safety issues and concerns in 2012 (5), and in the intervening time, any associated safety risks have been more thoroughly appreciated and are now readily mitigated using modern equipment and procedures. Although hydrogen is flammable (flammable range: 4–75% v/v in air) with a low minimum ignition energy (0.017 mJ at 20% v/v), today’s GC–MS systems are engineered with multiple layers of safety. Features such as flow-limiting frits, pressure and flow setpoint alarms, automatic system shutdowns, and automated oven venting mechanisms effectively prevent gas accumulation and ensure safe operation. Hydrogen generators further enhance safety by producing gas on demand from deionized water via proton exchange membranes, eliminating the need for high-pressure cylinder storage and reducing the volume of hydrogen present in the laboratory. Built-in safeguards include leak detection, overpressure relief, automatic shutdown to prevent “runaway” production, and minimal gas reservoir capacities, with gas being produced on-demand rather than being accumulated into an internal storage tank. In GC–MS systems, hydrogen’s high diffusivity and low viscosity are managed using high-capacity vacuum pumps and inert gas purging systems to prevent build-up in the ion source. The use of brass or copper tubing avoids embrittlement issues, and regular leak checks help to ensure gas line integrity.

Capital Cost of Laboratory Gas Generators and Return on Investment

Many of us will be familiar with the difficulty of raising capital expenditure for laboratory equipment, so whilst the price of helium remains relatively stable, the imperative to change remains lower.

Figure 1 shows the quarterly helium bulk purchase price from late 2023 to mid-2025, which indicates that the market price of helium continues to rise, and it is unlikely that we, as end users, are likely to escape some of that cost being passed on to us. Given the current cost of helium cylinder supply, a return on investment (ROI) estimate for the capital purchase and associated running costs of a gas generator vs. continuing supply via cylinders can be easily calculated for a laboratory with moderate helium usage. In the model, we have also included the ROI for nitrogen generation within the laboratory. Clearly, the ROI calculation for your laboratory will need to be calculated locally, but your supplier can help with this.

Assumptions used to build the ROI model:

Generator Costs

• Hydrogen gas generator cost: $24,000
• Replacement of deionizer (DI)cartridge (per annum): $299
• Service contract (per annum): $1000
• Electricity supply (per annum): $200
  Initial cost $24,000, annual costs $1499
• Nitrogen gas generator cost (with compressor): $20,000
• Replacement of filter(s) (per annum): $299
• Service contract (per annum): $1000
• Electricity supply (per annum): $200
  Initial cost: $20,000, annual costs: $1499.

Cylinder Gases

• Cost of hydrogen tank $(×2/month): $600
• Cost of helium tank (×2 /month):$1200
• Cost of nitrogen tank (×2/month): $450
• Monthly delivery cost: $50
• Monthly installation: $25
• Replacement of gas filters (per annum): $500
• Gas safety inspection (per annum): $250
  Helium annual cost: $1650, hydrogen annual cost: $1250

Figure 2 shows ROI of a hydrogen gas generator against helium cylinders in year two and against hydrogen cylinders in year three, which matches estimates from the major gas generator manufacturers. Nitrogen generators produce ROI against cylinder supply between years three and four, which again is in line with literature estimates.

In our experience, gas generator manufacturers are very capable of helping to select the correct specification for gas purity and supply requirements against your laboratory instrument and application needs, and will be able to assist with ROI calculations and compliance with all local safety regulations.

Sustainability of Carrier Gas Supply

Sustainability is a growing concern with many laboratories and switching from helium to hydrogen or nitrogen can help improve green credentials. For example, a GC instrument requiring helium at 1 L/min in a laboratory operating 12 hours a day, 23 days a month, could eliminate the delivery-related emissions of around 24 cylinders per year by using a hydrogen generator instead. In addition, helium production on average produces 500g CO₂/L, whereas using a typical hydrogen generator—which uses 0.787 kWh at 0.5 L/min—could result in significant CO₂ reductions. Again for a laboratory with average helium use, the CO₂ offset may be calculated as:

Generator: 0.5 L × 60 min = 30 L/h @ 0.787 kWh = 0.168 kgCO₂ ; 12 h @ 30 L/h = 2 kg CO₂

Helium cylinders: (500 g × 360 L) = 180 kg CO₂

This highlights the potential CO₂ emission reduction when switching to a hydrogen generator on a laboratory scale; however, this does not consider any transportation or manufacturing emissions. With generators, this is a one-timedelivery compared to repeated cylinder deliveries, which is also favorable for the reduction of CO₂ emissions with laboratory gas generation.

Requirements for Method Translation

To produce equivalent separations using an alternative carrier gas, some changes are required to the method parameters—primarily to account for the differences in gas viscosity and diffusivity. Further, one may want to take advantage of the increased inherent efficiency of hydrogen as a carrier gas and decrease analysis times whilst maintaining separation quality. Figure 3 shows that the van Deemter minimum (highest efficiency, narrowest chromatographic peaks) for hydrogen carrier gas occurs at higher linear velocity (40–60 cm/s), and nitrogen is most efficient in the lower linear velocity range (10–20 cm/s). As a result of the difference in gas viscosities (Figure 3, right), the pressures used within the gas chromatograph need to be adjusted to obtain similar selectivity and resolution. This task may seem daunting to even the more experienced GC practitioner; however, there are many sources of assistance for achieving the correct method conditions, including method translation software from the GC column and instrument vendors.

The Use of Hydrogen in GC–MS

Much is written on the safety and performance of hydrogen as a carrier gas for GC–MS applications; however, hydrogen is a viable and increasingly attractive alternative to helium for GC–MS. While it presents some chemical and physical challenges, these can be mitigated through intelligent system configuration, ensuring that performance, reproducibility, and safety remain uncompromised. Hydrogen’s lower viscosity and high diffusivity lead to lower head pressure requirements, and when combined with the detector being at vacuum, this may need some careful management to keep GC head pressures high enough to be manageable by the instrument. Systems may require column dimension adjustments, for example, shorter lengths or smaller internal diameters, to maintain optimal flow conditions while preserving chromatographic resolution, as shown in Figure 4.

Furthermore, hydrogen’s lower viscosity and higher diffusivity makes it more difficult to evacuate from the detector using vacuum compared to helium. It requires higher capacity turbomolecular or scroll pumps to prevent background accumulation, which are features of many newer GC–MS systems as manufacturers anticipate the switch in carrier gas. In addition, some systems incorporate inert purge gas, for example, N₂, venting systems to flush the ion source during shutdowns or vacuum loss, ensuring safe restart.

Hydrogen introduces specific challenges in electron ionization (EI) mass spectrometry (MS). As a result of its reducing nature, some compounds, including nitroaromatics and chlorinated solvents, can undergo in-source hydrogenation, leading to spectral artefacts and deviations from standard, for example, NIST, spectral library matching. Despite this, laboratories can address the issue through:

• the use of inert ion sources to suppress unwanted reactions
• the use of source components optimized to improve evacuation of the hydrogen from the ion source and reduce analyte residence times
• custom-built hydrogen spectral libraries
• updated tuning conditions.

Switching to hydrogen carrier gas for GC–MS applications is a viable alternative from a practical perspective, although a little more care and attention is required for method translation, and some operational or equipment updates may be required.

Considerations When Using Nitrogen as an Alternative Carrier Gas

Nitrogen is best suited for simpler separations, where very high efficiency is not relied upon to separate multiple components. Nitrogen of a suitable purity can be produced via laboratory generators and offers high efficiency at lower flow rates, and whilst this may result in longer analysis times, this is generally not significant in terms of laboratory operating efficiency. Nitrogen’s inertness and low cost make it attractive for a flame ionization detector (FID), a thermal conductivity detector (TCD), or a nitrogen phosphorous detector (NPD), but it is not suitable for MS because of poor sensitivity with electron ionization, typically producing limits of detection that may be orders of magnitude higher than with helium.

High purity nitrogen generators are available for the generation of carrier gas, operating either by pressure swing adsorption, which use a carbon molecular sieve to selectively adsorb oxygen and other impurities from compressed air, thereby allowing nitrogen to pass through, or by membrane permeation in which compressed air passes through a hollow fibre membrane, where oxygen, CO₂, and water vapor permeate out faster than nitrogen, leaving an enriched nitrogen stream.

Conclusions

Laboratories clinging to helium face growing exposure to price volatility and sustainability concerns. The real question is no longer if we can switch—but how much longer can we afford not to? And with the global helium supply landscape becoming more unpredictable and the pressure to adopt sustainable laboratory practices gathering momentum, it is perhaps time to reframe the conversation, not as a disruption, but as an overdue evolution in gas chromatography.

References

(1) Responding to The U.S. Research Community’s Liquid Helium Crisis, A Science Policy Report by American Physical Society, Materials Research Society, American Chemical Society, 2016.

(2) United States Geological Survey. Mineral Commodity Summaries; U.S. Department of the Interior, 2025.

(3) Helium One. Helium Market. https://tinyurl.com/49kh879y (accessed 2025-07-21).

(4) Helium Market Size, Share & Trend Analysis Report by Phase (Liquid, Gas), by Application (Cryogenics, Leak Detection, Welding), by End Use (Medical & Healthcare, Nuclear Power), by Region, and Segment Forecasts, 2025–2030; Grand View Research, 2025. https://tinyurl.com/mjdncp47

(5) Hinshaw, J. V.; Taylor, T. The Helium Crisis. LCGC International, 2012. https://www.chromatographyonline.com/view/helium-crisis (accessed 2025-07-15).

(6) Taylor, T. Is Hydrogen the Only Viable Gas Chromatography Carrier Gas for the Long-Term? The LCGC Blog 2019 https://www.chromatographyonline.com/view/lcgc-blog-hydrogen-only-viable-gas-chromatography-carrier-gas-long-term (accessed 2025-08-14).

(7) Hinshaw, J. V. Column Connections. LCGC Asia Pacific 2009, 12 (2), 1100.

(8) Hinshaw, J. V. Hydrogen Carrier Gas and Vacuum Compensation. LCGC Eur. 2011, 24 (1), 26–31.

Tony Taylor has worked as a chromatographer in the pharmaceutical, polymer, contract analysis, and consulting industries for more than 35 years. His experience includes; HPLC(–MS) and GC(–MS) method development, validation, and troubleshooting, and he currently leads the technical team at Element Laboratory Solutions. Tony is a founder of CHROMacademy and has delivered training in chromatographic analysis to thousands of students globally.

Emma Poole is a technical business development specialist with Element Laboratory Solutions (UK). Her background is in small molecule method development in the pharmaceutical industry using liquid chromatography and gas chromatography. She has spent the last five years in industry building and improving her knowledge of chromatographic techniques, both practically and theoretically.

Josep Serret is the technical development manager at Element Materials Technology (EMEAA). He joined when the company was known as Crawford Scientific, where he served as a trainer and a technical business development specialist. As part of the technical team, Josep supports our customers with method optimization, troubleshooting, and implementation of novel chromatography technologies.