Gas Chromatography & GC-MS – Troubleshooting & DIY

Optimizing Gas Chromatography & GC-MS

GC-MS has become the gold standard for routine chemical analysis and definitive identification. But it has reputation as a time consuming technique, and lab productivity is commonly bottle-necked by the GC. Fortunately, you don’t need to purchase a second GC to increase your throughput, because there are several ways to speed things up.

Optimizing your GC method can save you hours each day, so it’s important for your lab to get the most out of your equipment. A stock GC configuration with a default method can take 40 to 60 minutes. But a fifteen minute run-time is a realistic goal for most labs.

Labs that analyze the same few compounds every day – like production labs – will be nearer to ten minutes. Labs which only perform analyses within the same category – such as research labs – will be closer to fifteen minutes. Labs which need to cover a broad range of possibilities – typically forensics labs – will have the longest times, but even these should complete in under twenty minutes.

Now that you know what’s possible, let’s talk about how to get there!

Carrier Gas

The three main choices of carrier gas are helium, nitrogen, and hydrogen. Each choice has certain advantages and disadvantages, but the main points to consider are cost, safety, effectiveness, and speed.

Nitrogen is the most commonly used gas. As the most abundant gas in the atmosphere, Nitrogen’s main advantage is that it’s the cheapest carrier gas. Its biggest disadvantage is speed, so it tends to work best in labs where the GC sees only occasional use but doesn’t run constantly. That slow pace is the reason nitrogen has the best column efficiency, so it can be a good choice for tough separations – but you can achieve the same result by optimizing other components. So when the lab-work is being is held up at the GC, the first thing you consider should be switching to a different carrier gas.

Of the three gases, Hydrogen offers the greatest speed advantage. It comes with a reasonable cost, and its physical properties make it well-suited for use across a wide range of speeds, which gives it greater flexibility. Hydrogen can function well equally well anywhere from 20 to 80 cm/s. By comparison, nitrogen’s column efficiency drops off sharply at any velocity except 10 cm/s. This versatility allows for the fastest separation of many different compounds with methods optimized for the target analyte. Hydrogen easily stands out as the best overall choice for a carrier gas, but its primary disadvantages are safety concerns.

Important! Hydrogen is a widely-used carrier gas with virtually no risk to trained professionals when properly implemented. But proper implementation does require an initial investment in specialized equipment. The greatest risk is posed by using a tank of compressed hydrogen. By opting for a hydrogen generator, the gas is never pressurized and the risk of self-ignition is removed. The remainder of the risk can be mitigated by using a nitrogen purge or hydrogen detector to guard against leaks.

Important!Important! We advise against hydrogen as a carrier gas in academic labs where introductory training occurs with limited supervision.

Helium represents something of a compromise between nitrogen and hydrogen. It has a significant speed advantage over nitrogen; it’s almost as versatile as hydrogen; and as a noble gas, it’s the least reactive. Helium offers a number of advantages over nitrogen, without needing hydrogen’s risk management or special equipment. Its most significant disadvantage is cost: helium is fairly expensive due to its high demand.

Important!  A note on helium as a resource, as there has been some misplaced concern about “depleting” the planet’s helium supply – it’s not possible.
As a product of abundant underground radioactive alpha decay, helium accumulates in pockets which replenish themselves (unlike other gases). It then escapes the planet’s gravity at a constant rate due to its low mass, so the earth will continue to produce and lose helium at about the same rate for millions of years whether we use it or not.
That means the supply of helium is not a depleting well whose bottom draws ever nearer. The most accurate analogy would be a flowing river from which we can draw a steady, but finite amount.

Flow Rate

Your flow rate can be controlled in two modes: constant flow or constant pressure. We recommend constant flow, because constant pressure leads to wide variations in flow, and most of calculations in GC are based on flow rate. Each carrier gas can operate within a specific range of velocities without losing column efficiency.

Column efficiency is a measure of how much benefit you’re getting out of the column. Think of it like this – if you blast your carrier gas through the column, the molecules will be travelling too quickly to interact with the column. Those interactions are responsible for separation, so your peaks will be closer together than you’d expect from just shortening the run.

Nitrogen gas has the best column efficiency between 10 and 15 cm/s, reaching a maximum at about 12 cm/s. Helium’s optimum column efficiency ranges from 15 to 40 cm/s, while peaking at 20 cm/s. Hydrogen has the largest optimum range, spanning 20 to 70 cm/s, with best results at about 40cm/s.

GC Column

Choosing a column might seem complicated, but it’s really no different than the experience you might have when buying toothpaste. There seems to be a staggering number of choices! But once you cut past all of the fluff, you discover that they’re all just slight variations on two or three products made by the same company. So we’re going to make the decision as straightforward as possible, because if you wanted information overload, you’d probably be reading their product sheets instead.

First, let’s choose a stationary phase by determining whether your samples are normally polar or nonpolar.

  • Nonpolar: Use a polydimethylsiloxane (PDMS) column
  • Polar: Use a polyethylene glycol (PEG) column
  • Somewhere in between: Use a polyethylene glycol (PEG) column
  • Combination / unknown: Use a 50% phenyl column
  • Quant only, no separation: Choose the opposite of your sample (faster analysis)

Next, we can turn our attention to the film thickness. If your sample identity and concentration are usually unknown to you, choose a thicker film (about 1 µm). You’ll gain better separation and a greater tolerance for high concentration samples at a slight cost in speed. If you know your analytes and already have good separation, shorten your run times with a thinner film (about 0.1 to 0.25 µm).

A 0.25 mm inner diameter is ideal for most labs. Deviating from this without good reason can introduce problems.

A standard column length is 30 meters. A longer column will give you better separation, but slow your analysis times. If your configuration already has a good separation efficiency, reduce your run times by shortening your column. If you’re not familiar with column cutting, ThermoFisher has an excellent guide.


As the GC’s temperature rises, more components of the sample will enter the gas phase and travel down the column. If you’re not getting enough separation, a temperature ramp can introduce sample components more gradually. Ramps can also be used to sharpen peaks for better quantification. But keep in mind that molecules can become unstable and break apart if the temperature is too high. That also includes your column coatings, so always check its specifications before raising your oven temperature.

Raising the temperature beyond your sample’s thermal stability will cause it to degrade, and molecules that are too large to enter the gas phase directly will only appear as fragments. It’s important to recognize this when it occurs to prevent making false identifications. Although thermal degradation will make any peak integration meaningless,  with enough experience you’ll be able to identify the parent molecule from the puzzle pieces. The next technique – derivatization – is especially useful in these situations.

Derivatization / Internal Standardization

Sometimes you might encounter a sample that seems like it could almost run, but doesn’t. It may go undetected, fragment as described above, or leave molehills instead of mountains on your chromatograph. These aren’t issues that can be fixed by making adjustments to your GC, and this is where derivatization comes in. It picks up where other methods leave off: so long as your sample doesn’t run the risk of out-right damage to the instrument, you have options to make it viable.

By subjecting the sample to a chemical reaction, you can change the chemical structure into a derivative that’s better suited for analysis. But derivatization isn’t just for samples you can’t run – you can also use it to produce derivatives with shorter analysis times! There are more reactions than we could ever list here – entire books have been filled with the possibilities. Fortunately for you, we have those books! Contact us for assistance if you need help with this technique.

Internal standardization is a technique that’s better suited to GC than GC-MS. This can help you to determine something elusive that can’t normally be detected using FID – like the precise concentration of water in a set of serial dilutions. By spiking your water with a detectable compound (one which won’t interfere with further analysis), you can quantify concentrations much more accurately.

Sample Concentration

For both data quality and instrument longevity, you should aim to use the smallest detectable sample size possible. This is usually within the 1-100 ppm range, favoring the lower end. Dilution calculations are very straight-forward: m1v1=m2v– just remember to account for the dilution factor in your final analysis.

Some labs won’t always have total control over the concentration of the samples they receive, or even prior knowledge of their contents. This is normally the case in forensic labs. In these cases, other methods can estimate the sample concentrations before introducing it to the sensitive components of the GC. If you place a highly concentrated sample on an FT-IR or a UV-Vis, the worst that can happen is a saturated graph.

Concluding Points

While your GC offers plenty of room for optimization, all of these factors interact with one another – so take care to avoid making multiple changes at once. For example: while changing your carrier gas and adjusting your flow rate are both ways you can improve your performance, making both of those changes together can actually worsen your performance.

This guide is intended to help you get the biggest improvement possible in the shortest amount of time. But the reality is that bringing your GC to highest potential will require a bigger time investment, some careful planning, and plenty of calculations. But that’s what we’re here for, so don’t hesitate to contact us. If you’re the type who likes to dive into the details, we can provide you with the resources and guidance you need. If not, we can schedule a visit and get your GC running better than ever.


Troubleshooting Gas Chromatography & GC-MS

My peaks keep showing up later and later every time I run a sample! (Retention Creep)

You probably need to change your septum. Certain brands wear out very fast, so this can catch you off-guard after switching if you’re used to a more durable brand. If changing the septum doesn’t fix the issue, secure or replace other vulnerable seals. If that still doesn’t fix it, ensure that your gas pressure and oven temperatures are where they should be. Also ensure that the run is being started consistently every time.

My peaks aren’t sharp enough to quantify! (Peak Tailing / Fronting)

As long as your installation hasn’t changed recently, this usually indicates a problem with the sample itself. Your sample concentration might be too high for that compound, or the sample could have poor compatibility with the column. Try diluting the sample, derivatization, or changing the column.

My peaks are running together! (Poor separation)

Follow the GC Optimization guide on this page to learn how you can improve your peak resolution and run time.

My chromatograms trail up into an S shape at the end of the run! (Column Bleed)

If you start to notice column bleed, it generally means that you’re falling behind on your maintenance, so it won’t hurt to give your GC a full tune-up. First, bake out your column by running it at the flow rate maximum and isothermal temperature limit for about 20 minutes. Start by replacing your short-lived components (seals, septa, and o-rings), then change your gas filters and trim your column ends by a few cm. Reassemble everything with extra care, and double check for leaks. If the bleed still continues, then your column is just worn out and needs replaced.

My peaks have peaks! (Split Peaks)

This is usually a problem with injection or vaporization. If it’s happening consistently for multiple users, then check ensure that the injector port is reaching the correct temperature, and verify that your solvent is compatible with your column. If it’s more intermittent, try injecting a lower volume more slowly (1 ppm & 1 µL should  be your guideline). If this still doesn’t fix it, consider adding wool to the injection port. This increases the surface area and aids rapid dispersion and vaporization.

My analyte isn’t showing up! (Unsuitable Samples)

GC-MS is a powerful technique, but it does have limitations. A general guideline is: if you can’t smell it, you can’t run it. Samples with high molecular weights (such as a heavy oils) are also unsuitable. When a molecule is too heavy to vaporize, you’ll never see the full molecule on the chromatograph. You’ll only see fragments of its thermal degradation – and you’ll continue seeing them until the sample fully degrades.

Important! Salts, ionic solutions, and metals are absolutely out of the question!

There’s something wrong with this GC Injection Syringe!

Even carefully maintained and properly used syringes wear out quickly with normal use, so it’s best to consider your syringes as consumables. Injection syringes are extremely fragile, and prone to failure at the slightest misuse. Mildly corrosive samples can jam up a syringe pump in a matter of seconds when introduced to the high temperatures of the injection port.

Proper cleaning includes flushing the syringe with an appropriate solvent after every sample. Follow this with water and several acetone rinses, and then place the syringe back into its case.

We recommend that you always have spares on-hand. Replacement parts can be helpful, but undetectable flaws can make it difficult to change them without accidental damage to the new parts. It doesn’t take many bent replacements before it becomes cheaper and less frustrating to simply have an extra.


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