The switch from Helium as a carrier gas

Helium Production and Supply Chain Challenges

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, with chromatographic and spectroscopic uses accounting for approximately 15% of global usage [1]. Despite global helium reserves estimated at 31.3 billion cubic meters [2] - enough for over 180 years at current usage [3] - frequent localised 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 in1996 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 focussed efforts on developing equipment which is 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(MS) instruments and applications have been converted to alternative carrier gases.

Why haven’t we made a wholesale switch?

The question then is why? Well perhaps we analytical chemists have short memories. 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. In fact, safety may not be the primary barrier to switching from helium to alternatives like 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 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 towards more sustainable practices in analytical laboratories. 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 deionised 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: Estimated helium bulk purchase costs (USD per metric ton) in Germany, UK and the USA, 2023 to 2025

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 versus 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 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 $(x2 / month) $600
Cost of helium tank (x2 / month) $1200
Cost of nitrogen tank (x2 / 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 $1250

Figure 2: 5-year return on investment estimates for laboratory gas generation versus cylinder supply

Figure 2 shows ROI of a hydrogen gas generator against helium cylinders in year 2 and against hydrogen cylinders in year 3, which matches estimates from the major gas generator manufacturers. Nitrogen generators produce ROI against cylinder supply between years 3 and 4, 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 as labs requiring helium gas for their GC instrument to meet 1LPM (liter per minute) demand for a lab operating 12 hours per day, 23 days per month can save on the delivery associated emissions of 24 cylinders year with a hydrogen generator. Additionally, helium production on average produces 500g CO₂/L whereas using a typical hydrogen generator which uses 0.787 kWh at 0.5L/min could result in significant CO₂ reductions. Again for a laboratory with ‘average’ helium use, the CO₂ offset may be calculated as;

Generator: 0.5L x 60 min = 30L per hour @ 0.787 kWh = 0.168kgCO₂ ; 12 hours @ 30L/h = 2kgCO₂

Helium Cylinders: (500g x 360L) = 180kgCO₂

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-time delivery compared to repeated cylinder deliveries which is also favorable to 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: Common GC carrier gases typical vanDeemter curves (left) and temperature / viscosity relationship (right)

Figure 3 shows that the vanDeemter minimum (highest efficiency, narrowest chromatographic peaks) for hydrogen carrier gas occurs at higher linear velocity (40-60cm/sec) and nitrogen is most efficient in the lower linear velocity range (10-20 cm/sec). Due to the difference is 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.

Figure 4: in silico method translation (including oven temperature program) when switching from helium to hydrogen which produces equivalent chromatography with a reduction in analysis of over 2 mins (adapted from Agilent Technologies application note 5994-7408, May 2024)

Figure 4 shows the inherent efficiency of hydrogen which produces an equivalent separation at higher linear velocity and flow rate than the original helium separation. No other methodological changes were required to achieve this separation. Alternatively, the conditions could have been translated to produce a superior separation in the same time frame as the original, again the method translation software can be used to indicate the new method conditions required.

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 in order to keep GC head pressures high enough to be manageable by the instrument. Systems may require column dimension adjustments (e.g. shorter lengths or smaller internal diameters) to maintain optimal flow conditions while preserving chromatographic resolution as shown in Figure 5.

Figure 5: Plots of inlet pressure vs. column length, with hydrogen carrier gas and vacuum compensation. Column inner diameters (mm): (a) 0.20, (b) 0.25, (c) 0.32, (d) 0.53; column temperature: 50 °C; average linear velocity: 40 cm per s. The blue shaded area designates negative inlet pressures.

Further, 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. Additionally, some systems incorporate inert purge gas (e.g. N₂) venting systems to flush the ion source during shutdowns or vacuum loss, ensuring safe restart.

Hydrogen introduces specific challenges in electron ionisation (EI) MS. Due to its reducing nature, some compounds (e.g. nitroaromatics, chlorinated solvents) can undergo in-source hydrogenation, leading to spectral artefacts and deviations from standard (e.g. NIST) spectral library matching. Despite this, laboratories can address the issue through:

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

Over many years, we have been supporting customers to switch to hydrogen carrier with GCMS applications, and whilst a little more care and attention is required to method translation and some operational or equipment updates may be required, it is a viable alternative from a practical perspective. Figure 6 shows a successful translation to hydrogen for the analysis of pesticides in pigmented foods.

Figure 6: Method translation for the GC-MS determination of pesticides in pigmented foods showing improved chromatographic resolution, issues with reduced library matching results due to spectral changes in EI mode (bottom left) and in ion-source reactivity which can be overcome using an inert EI source (bottom right) (adapted from Agilent Technologies application note 5994-6505, July 2023)

We can see from Figure 6 that using hydrogen carrier with a translated method provides higher resolution for the MS/MS pesticide determination, however we can also see that there is a reduction in library match quality for chlorpyrifos-methyl (bottom left) when using a standard ion source in the mass spectrometer. When using an inert source the library match is improved as well as showing a reduction in hydrogenation of the nitrated analyte tecnazene (bottom right). It is possible to adapt most standard ion sources for improved use with hydrogen carrier – check with your vendor for more details.

Considerations when using nitrogen as an alternative carrier

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 flame ionisation (FID), thermal conductivity (TCD), and nitrogen phosphorous (NPD) detectors, but it’s not suitable for MS due to poor sensitivity with electron ionisation, typically producing limits of detection which may be orders of magnitude higher than with helium. In applications such as blood alcohol testing, nitrogen-translated methods using adjusted flows and oven profiles still achieve regulatory compliance specification as shown in Figure 7. It should be noted that in this particular application, the translation to nitrogen carrier has not led to any significant increase in analysis time.

Figure 7: Chromatograms of a 50 mg/dL injection of the Agilent Blood Alcohol checkout mix using nitrogen carrier gas (adapted from Agilent Technologies application note 5994-6508, July 2023)

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, allowing nitrogen to pass through or by membrane permeation in which compressed air passes through a hollow fibre membrane, where oxygen, CO₂, and water vapour permeate out faster than nitrogen, leaving an enriched nitrogen stream.

Conclusions

Perhaps we are just naturally resistant to change and have short memories when it comes to the pain of supply restrictions. Perhaps we are scared by the safety and scientific barriers to switching to an alternative carrier gas. Perhaps inertia in face of other priorities takes precedence, but it is certain that, for laboratories who wish to explore alternatives to helium, both hydrogen and nitrogen present viable and increasingly attractive options. Hydrogen offers excellent chromatographic efficiency and faster run times due to its superior physico-chemical properties, while nitrogen provides an inherently safer, inert, and perhaps more familiar choice - particularly for applications where lower numbers of analytes are being analysed or ultra-high resolution is not required. We have shown that, with appropriate method translation and modest equipment adjustments, laboratories can maintain analytical performance with either gas. Hydrogen requires additional safety considerations, but modern generators and GC(MS) systems have built-in safeguards to make its use in analytical settings entirely practical. Nitrogen, meanwhile, poses fewer risks and is well suited for detectors like FID, TCD, and ECD, though less so for MS due to lower inherent sensitivity with EI sources. Ultimately, the choice of carrier gas depends on a lab’s analytical requirements, safety culture, and cost priorities. With careful evaluation and support from vendors and method tools, transitioning from helium is not only feasible - it can be a forward-thinking step toward greater efficiency, security of supply, and sustainability.

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.

Resources

[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, 2025

[3] Helium One (accessed 21st July 2025)

[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 (accessed 15th July 2025)

[5] J.V. Hinshaw, T. Taylor, The Helium Crisis, LCGC International, November 2012 (accessed 15th July 2025)

Authors;

Tony Taylor - Technical Director, Element Lab Solutions, Strathaven, UK

Josep Serret - Technical development Manager, Element Lab Solutions, Strathaven, UK

Emma Poole - Technical Business Development Specialist, Element Lab Solutions, Strathaven, UK