Looking with Light: Understanding Gas Chromatography, Part I: Gases

Published on: 
Cannabis Science and Technology, November/December 2021, Volume 4, Issue 9
Pages: 12-19

Columns | <b>Navigating the Lab</b>

Let’s take a deeper look into GC instrumentation.

Gas chromatography (GC) is a well-established chromatography technique in analytical chemistry. Over its almost 50-year history the technology has improved and changed to accommodate a wide variety of compounds and targets. As we see in liquid chromatography, many analysts do not have a deep understanding of the functioning and chemistry of GC systems and often depend upon methods they find from manufacturers or technical sources and adapt them to their analyses. In this column, we will take a deeper look into the chemistry, physics, and methodology of each piece of GC instrumentation starting with the gases that compose the mobile phase. Over the next few columns, we will look at the different components of the GC system (form and function) to see what changes can be made to increase resolution, efficiency and produce better analyses.

Gas Chromatography Targets

There are several general conditions for samples to be amenable to the most common gas chromatography (GC) system configurations: 

  1. The samples and compounds must be volatile. Volatility is the ability of a substance to vaporize at a given temperature and pressure. Substances with high volatility usually exist as a vapor while low volatility samples exist as liquids or solids. Low volatility substances resist evaporation (liquids) or sublimation (solids) at atmospheric temperatures and pressures. Samples should be volatile at temperatures below 400 °C. The boiling points of these targets usually need to be less than maximum temperature of the GC columns or system in which they are used. So, if a GC column has a maximum temperature of 200 °C, then targets with boiling points over the 300 °C range will probably not be good candidates for analysis with that column.
  2. Samples for gas chromatography must be volatile but also thermally stable. Thermostability is the ability of a substance to resist chemical, physical, or structural changes such as polymerization or decomposition when exposed to high temperatures, meaning the samples must be able to vaporize without breaking down in the high temperatures of the GC injection port. 
  3. Samples or substances should be unreactive with the GC system; they should not participate or cause reactions within the chromatographic pathway.

Boiling Points and Vapor Pressure

Volatility is not a defined measurement, but it is often a reflection of the vapor pressure or the boiling point of a substance. Vapor pressure is a measurement of how a substance changes from a condensed form to a vaporous form. Sometimes the term vapor is used interchangeable with gas or confused with an aerosol. Gases are one of the states of matter (solid, liquid, and gas) with a single form at room temperature. An aerosol is a gaseous form which contains both liquids and solids in fine particles or droplets. A vapor is the gaseous stage or state of a substance, which can be present with other states of the substance at the same time at the same temperature. Vapor pressure is the measurement of the equilibrium between vapor and condensed forms of a substance when confined in a sealed vessel. Volatile compounds exist more in the vapor phase of the system and therefore have a higher overall vapor pressure.

Boiling point, on the other hand, is related to vapor pressure in that it is the temperature at which the vapor pressure of a liquid is equal to the pressure around it and this temperature induces the liquid to evaporate quickly (boil). Most boiling points are recorded at atmospheric pressure. Boiling point can be affected by a variety of factors including polarity, molecular weight, and molecular or atomic interactions. The lower the boiling point of a substance, the more time it spends in the gaseous mobile phases and speeds more quickly through the chromatographic system. Very low boiling point substances like some solvents are virtually unretained on the stationary phase of columns, which make them good substances to dissolve GC samples. Generally, solvents with boiling points lower than the starting temperature of the GC method will quickly pass through the system as unretained, while solvents that have boiling points higher than the starting temperatures will possibly be retained on the stationary phase and produce a retained peak (Table I). Many GC column chemistries have retentions that reflect elution by either increasing molecular weights of the analytes or increasing boiling points which can help the chromatographer during method development.

GC System Configurations

The general configuration of a gas chromatography system starts with the carrier gas which is either contained in a cylinder or produced using a gas generator depending on the type of gas. Cylinders containing flammable gases such as hydrogen are commonly threaded in the opposite direction of nonflammable gas cylinders to prevent common mix-ups. The gas is controlled by a flow controller or a regulator and is plumbed into the GC system usually near the injection port. The injection port is the entry into the system for samples and connects to the column. Gas flows through the injection port and then the column allowing for the partitioning of analytes between phases. The final components are the detectors, which output an electronic signal to the chromatograph and the waste for the system (Figure 1).

Gas chromatography systems are plumbed to a variety of gases depending on the detectors and type of analysis. A carrier gas is common to all the most commonly used configurations. The carrier gas is the mobile phase, which carries analytes to the column for partition chromatography. Most gas lines are plumbed from either a cylinder, dewar, or generator with a series of filters or traps intended to trap any contamination or potential compounds which could interfere with analysis. 

The most common traps for GC systems include an oxygen trap, a moisture trap, and a hydrocarbon trap. The oxygen trap removes oxygen from the purified gas that could damage the GC column. Oxygen traps are often composed of metal and an inert reagent. The goal of the trap is to reduce oxygen concentrations to below 20 ppb. Many oxygen traps can remove small organic molecules and sulfur from the gases. 


The moisture trap removes water and other moisture vapors from the system that could impede vaporization of the samples. Moisture or water traps can often be refilled with sorbent materials instead of being replaced. The body of a trap is plastic, glass, or some combination of both rated to withstand gas pressures of the GC system. Plastic traps may pose a risk of contamination, so for applications where this may be of concern use glass bodied moisture traps. 

The hydrocarbon trap removes any potential hydrocarbon contamination from greases or oils which could be seen as peaks in the chromatogram. The trap sorbent is usually activated carbon or carbon media that removes organic solvents. The traps are in many cases metal and in some cases can be refilled instead of being replaced. 

GC gas traps can be offered in a variety of configurations including manifolds with space for all the traps or combinations of different functionalities in one type of trap. There are traps that contain indicators which change color when the contamination is detected or when the traps are depleted. Each configuration has its own benefits (that is, ease of use, longevity, and so on) and drawbacks (cost, time). In the end, the best trap is the one that gives the user the highest purity of carrier gas through their GC system.

Gas Purity

The gas purity needed for a GC system depends on the type of system and the level of sensitivity needed by the system. A gas chromatography–mass spectroscopy (GC–MS) system measuring low parts-per-million targets have higher sensitivity and therefore need higher purity gases than a flame ionization detector (FID) that only measures percent levels of components in a mixture. The cost of gases increases as the purity of the gas increases, therefore it is best to use the grade of gases suitable for the type of system used and the analytical range of the targets you wish to detect. The nominally recommended purities for the common gases such as helium, nitrogen, and hydrogen should be between 99.995% and 99.999% for most GC applications. 

Despite the grade of gas, the typical impurities of oxygen, water, and hydrocarbons should be below 1–2 ppm each. Other impurities such as carbon monoxide, carbon dioxide, and other gases are not often individually monitored but together with oxygen, water, and hydrocarbons should be less than 10 ppm. Gas suppliers can grade their gases in cylinders and containers in a variety of ways to indicate purity and potential use. Some designations of “grades” care more about marketing than industry standards, and the analyst needs to exercise care to distinguish the best product for their application. One company’s ultra-high purity helium may be called ultra-pure carrier gas grade. The official designation should state a numerical purity like N4 or %99.99 (also known as four nines) (Table II). Compressed gas cylinders usually maintain their certified values for purity down to only 10% of the original pressure. At lower pressures there could be higher levels such as impurities like water or hydrocarbons. 

The number of impurities in a GC system can also increase with the improper choice of the gas handing equipment and plumbing. GC systems should always be plumbed using stainless steel or copper tubing and fittings. Gas regulators should have stainless steel components impervious to oxygen and moisture. Many companies have purity ratings similar to the gases to indicate the number of impurities that may be introduced to the gases from the regulator. Impurities from regulators may include off gassing of materials inside the regulator, leaks which allow air into the system, and reactions between the materials of the regulator and the gases. The purity of the regulator should match the purity of the gases used.

Regulators routinely used in the laboratory are either single stage or two or dual stage regulators. Single stage regulators are not used in GC systems but can be used in gas lines that require continue pressure adjustments. Dual stage regulators are actually two regulators in one piece of equipment fixed to the gas cylinder. The first stage controls the pressure from the cylinder and the second stage reduces the pressure further to plumb into the GC system. The second stage keeps the pressure continuous even when the overall pressure of the cylinder drops.

Selecting Carrier Gases

The carrier gases for most GC applications are helium, hydrogen, nitrogen, or argon. There are four main considerations in the choice of carrier gas:

  1. Application;
  2. Efficiency; 
  3. Availability; and
  4. Cost

The application, type of column, and analysis can each dictate the type and grade of the required carrier or make-up gas. A make-up gas is an additional gas plumbed into the system to produce a specific effect on the detector or system. The lower in concentration of the potential target analyte, the higher the purity of carrier and make-up gas are needed for analyses. The higher the purity of gases, the higher the cost of the gas. 

The next consideration of efficiency deals with the chromatographic efficiency of the system and theoretical plates as was discussed in our previous chromatography columns. Efficiency is a measure of theoretical plates in a chromatographic system. As has been discussed previously, chromatography columns do not have physical plates that can be measured so the plates are theoretical to describe the efficiency of the column. This is called height equivalent to a theoretical plate (HETP) and is measured by the van Deemter equation in gas chromatography analyses (Equation 1).


where A is the eddy diffusion parameter, B is the longitudinal diffusion coefficient of eluting particles resulting in dispersion (m2/s), C is the mass transfer coefficient of resistance of analyte between mobile (m) and stationary phase (s), and u is linear velocity or speed (m/s).

The first term of the equation is the eddy diffusion parameter and refers to the diffusion or mixing of substances by a turbulent, swirling motion around objects. In certain types of columns where the stationary phase is particulate in nature, currents or eddies can form and create forces that effect the HETP. These types of columns include packed GC columns (Figure 2a). Columns that are tubular in nature (that is, capillary columns) do not have the same forces so the term A of the equation is zero (Figure 2b).

The second term B is the longitudinal diffusion coefficient which is the constant proportion of the diffusion of one component into another divided by the average speed of diffusion. This term is a calculation of the dispersion as a solute travels down the pathway. In this situation the concentration of the solute is highest in the middle of the pathway and more diffuse on the edges with the solute diffusing more as it passes through the column and contributes to band broadening (Figure 3). The diffusion effects are more pronounced at lower flow rates. Gas chromatography is more effected by these forces because of the exponentially higher diffusion coefficients found in gases as opposed to liquids. 

The third term is the mass transfer coefficient between the mobile and solid phase. Since the mobile phase (gas) is rapidly moving, an equilibrium may not be reached resulting in peaks being either less retained or retained too highly on the solid phase depending on the depth or thickness of the solid phase (film). The mass transfer is most efficient at lower flow rates, which is the opposite of the longitudinal diffusion. The most effective set of conditions is a balance between these two coefficients resulting in a minimal value for the HETP and the optimized linear velocity (u) in a van Deemter curve (Figure 4).

The window of velocity for the optimal velocity can change with the type of carrier gas, solid phase (film) thickness, and the inner diameter of the column. Film thickness can influence the mass transfer while smaller diameter columns produce flattened curves with optimal velocity at lower velocities. The B/u diffusion term is greatly influenced by the type of carrier gas. The goal is to optimize the balance between the type of gas, the gas flow, and the column dimensions to produce an area of optimal practical gas velocities (~1.5 to 2x the optimal velocity) in which the system operates.

Carrier gases and their own van Deemter curves will influence the optimization of the GC system. Helium is the one of the most commonly used carrier gases for GC due to its safety and relatively good van Deemter curve with a range of practical optimum gas velocities (OPGV) between about (25–35 cm/s). The drawback to helium is that it is an expensive commodity which is dependent upon the finite reserves of natural gas. There are no easy was to produce helium (especially within the average laboratory) and helium’s availability and cost in some cases offset its ease of use and safety.

Nitrogen is another potential GC carrier gas which unlike helium is fairly inexpensive and can be produced in-house with a liquid nitrogen dewar, or a nitrogen generator and purifier. Nitrogen is a fairly safe gas in the laboratory, but it is not the most optimal gas for GC with a smaller lower range OPGV from ~10 to 15 cm/s. 

Finally, hydrogen, like nitrogen is cheap, accessible, and easy to produce but can cause some safety concerns (real and exaggerated) in the laboratory. Hydrogen can be produced using a hydrogen generator or from hydrogen cylinders. Hydrogen has the best OPGV range of values with higher velocities from 35 to 60 cm/s, but there can be possible hydrogenation reactions that may affect some target analytes (Figure 5).

As I said earlier, there are safety concerns regarding the use of hydrogen in the laboratory as a carrier gas. Hydrogen can be explosive at above ~4% volume in air but on the positive side, it quickly diffuses, and most modern GC systems regulate flow and have automated safety shutdowns to prevent accidents. Secondly, there is very little hydrogen flowing through any GC system so the amount of possible leakage at the system is minimal compared to other possible leaks in the gas plumbing system upstream of the chromatograph. 

Final Thoughts

Each gas has its own positive and negative points for use in GC analyses. There can be applications that would benefit from a different type of carrier gas or even a mix of carrier gases. Many GC FID analyses may not need the purity and expense of helium and could perform better with hydrogen. In GC–MS analyses, the hydrogen may cause sensitivity issues or system reactions. In high-throughput laboratories, method run times could factor against using inherently slow running nitrogen (remember those optimal low velocities!). Some GC systems allow users to switch or blend gases, this is often controlled by the flow controllers in the inlet area of the GC which we will continue with in our next discussion of GC system components and functions. 

Further Reading

  1. P.L. Atkins, Cannabis Science and Technology, 4(3), 17-28 (2021). Modern Practice of Gas Chromatography, 2nd Edition, R.L. Grob, Ed. (Wiley: New York, 1985).
  2. D. Harvey, Contributions to Band Broadening in Chromatography | Image and Video Exchange Forum, 2013.
  3. W. Jennings, E. Mittlefehldt, and P.P. Stremple, Analytical Gas Chromatography, 2nd edition. (Academic Press, San Diego, California, 1997).
  4. D. Kealey and P.J. Haines, Analytical Chemistry; The instant notes chemistry series; BIOS: Oxford, 2002.
  5. H.M. McNair, J.M. Miller, and N.H. Snow, Basic Gas Chromatography, Third edition (Wiley: Hoboken, New Jersey, 2019).
  6. Gas Chromatograph, Available at: (accessed 2021 -11 -15).
  7. Van Deemter Equation. Wikipedia; 2021.
  8. P. Froehlich and K.Myers, "Helium or Nitrogen, Tank or Generator?" (accessed 2021 -11 -15).
  9. Airgas Catalog & Reference Guide;


PATRICIA ATKINS is a Senior Applications Scientist with Spex, an Antylia Scientific company and has been a member of many cannabis advisory committees and working groups for cannabis including NACRW, AOAC and ASTM.

How to Cite this Article

P. Atkins, Cannabis Science and Technology 4(9), 12-19 (2021).