Helium shortages and rising costs are forcing laboratories to rethink long-standing GC methods. This article draws on insights shared in the “Alternative Carrier Gas for GC and GC-MS” webinar, hosted by Separation Science and presented by Ed Connor of Peak Scientific. The session focused on how analysts can transition to hydrogen or nitrogen without compromising data quality, while also highlighting the specific hardware and method adjustments required for GC-MS workflows.
Why Labs Are Moving Away from Helium
Helium has long been the default carrier gas due to its inertness and performance. However, supply constraints and price volatility have made helium less practical for routine use.
Connor frames the issue directly. “Labs aren’t moving away from helium by choice—they’re being forced to, and the difficult part is making sure the method still works the way you expect once you change the gas.”
This shift creates a clear need for decision-making frameworks rather than one-size-fits-all replacements.
Hydrogen vs. Nitrogen: Choosing the Right Alternative
Hydrogen and nitrogen each offer viable paths forward, but they behave very differently in a GC system.
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“With hydrogen, you can often reduce run times—sometimes by 30–50%—because it operates at a higher optimal linear velocity, but you need to assess system safety and whether your analytes are reactive," Connor explains. “Nitrogen runs at a much lower optimal velocity, so you’ll typically see longer analysis times and broader peaks unless you adjust the method.”
Where labs often run into problems is treating hydrogen as a direct replacement. Without re-optimizing conditions, changes in selectivity or peak shape can compromise results, and in GC–MS systems, safety and compatibility need careful evaluation. Nitrogen poses fewer safety concerns, but performance losses can be significant if methods are not properly adjusted.
Labs should consider the following:
Feature | Hydrogen | Nitrogen |
Separation Speed | Faster | Slower |
Efficiency | Higher | Lower |
Stability | Compatible with many methods | Stable, inert |
Implementation | Requires safety controls and validation for reactive compounds | Easier to implement in conservative workflows |
The right choice depends on application priorities. High-throughput labs often favor hydrogen, while regulated environments may lean toward nitrogen.
The takeaway is straightforward: there is no universal replacement. Each gas introduces trade-offs that must be managed.
Impact on Method Performance and GC-MS Hardware
Switching carrier gases affects retention times, resolution, and peak shape. These changes require method revalidation, especially for GC-MS systems, where the physical properties of the carrier gas directly affect the detector.
“You can’t simply replace helium with another gas and expect identical chromatography,” emphasizes Connor. “You need to re-optimize linear velocity for that gas, adjust oven temperature ramps, and sometimes change column dimensions to recover resolution and peak shape.”
When moving to hydrogen, GC-MS users must make specific hardware considerations:
- Vacuum pump efficiency: Hydrogen is much lighter than helium. Analysts must ensure their vacuum pump can handle hydrogen, as it will have a harder time clearing the gas from the ion source.
- Ion source material: Connor recommends switching to low-nickel ion sources, as nickel can facilitate unwanted hydrogenation reactions and increase background noise.
- Draw-out lenses: Upgrading from a standard 3mm draw-out lens to a 6mm lens can help reduce the volume of hydrogen in the source, improving overall sensitivity and minimizing changes in fragmentation patterns.
The bottom line: performance can match or exceed helium—but only with proper optimization and hardware adjustments.
Practical Steps for Switching Carrier Gases
Successful transitions require a structured approach. Labs that treat the switch as a controlled method change avoid the most common pitfalls.
“Start with a method where you understand the critical performance criteria, then switch the carrier gas and re-optimize step by step,” offers Connor. “Monitor retention times, resolution, and peak shape at each stage before rolling the change out more widely.”
To mitigate potential signal-to-noise reductions—which can drop by a factor of 2 to 5 with hydrogen—Connor strongly recommends using selected ion monitoring (SIM). “Wherever possible, if you're using GC-MS, it’s advisable to use SIM detection. This goes a long way to overcoming the sensitivity issues surrounding the use of hydrogen, bringing performance very close to what you get with helium.”
A disciplined transition typically includes:
- Recalculating flow rates and pressure settings based on optimal linear velocity
- Utilizing SIM detection to recover sensitivity losses
- Running side-by-side comparisons with the original helium method
- Verifying detector response, MS vacuum compatibility, and adjusting hardware
- Documenting all changes for regulatory compliance
Successfully completing these steps ensures a robust and validated method conversion.
Application Impact: FAMEs, Pesticides, and PAHs/PCBs
While theoretical adjustments are important, Connor shares real-world examples demonstrating hydrogen's capabilities across various applications:
- FAMEs (fatty acid methyl esters): In a 39-component standard run on a GC-FID, Connor demonstrates that by matching the linear velocity of the new hydrogen method to the old helium method, analysts could achieve the exact same retention times but with sharper, narrower peaks due to hydrogen's superior efficiency.
- Pesticides: Using a 59-pesticide mixture, Connor shows that running hydrogen in SIM mode yielded excellent recovery rates (with the vast majority showing less than 10% RSD) and strong calibration linearity, proving hydrogen's viability for trace-level detection.
- PAHs and PCBs: The most dramatic improvement came in environmental testing. Traditionally, PCBs require a 60-minute analysis on a GC-ECD, whereas PAHs require 30 minutes with UV detection. By combining these methods on a GC-MS triple quad with hydrogen as the carrier gas, both groups of compounds were successfully separated and analyzed together in just 11 minutes. “This is a big potential time-saving for labs who are able to switch,” Connor notes.
Key Takeaways
Switching carrier gases is no longer optional for many labs. The decision now centers on how to manage the transition effectively.
The most important takeaways are:
- Hydrogen offers speed and efficiency but requires safety checks, hardware optimization, and verification of vacuum capacity.
- Nitrogen provides stability but slows analysis and may reduce resolution.
- Utilizing SIM mode and larger draw-out lenses can mitigate the sensitivity losses commonly seen with hydrogen.
- Dramatic time savings are possible, such as combining PAHs and PCBs into a single 11-minute run.
Connor summarizes the challenge: “The objective isn’t just to replace helium—it’s to demonstrate that the method still meets your original performance criteria, or improves on them, under the new conditions. That means proving equivalence in resolution, sensitivity, and reproducibility.”
Labs that approach the switch strategically can maintain performance while reducing dependence on helium.
Watch the on-demand webinar to access the complete expert perspective from Ed Connor and explore how these strategies apply to your workflows.
