Introduction to Gas Chromatography for New and Advanced Users – Common Gas Chromatography Problems

Firstly, I would like to thank you all for staying with me and sharing our GC blog in 2025. It is always a pleasure to share our experience and knowledge.

This last GC chapter in 2025 will be fully contributed to common GC issues and problem solving / prevention. Additionally, we will cover some simple practical tips for routine GC setup but also some steps you can utilize in aid of GC method(s) development.

How do I set up my GC for Routine Analysis?

There are few critical gas chromatograph sections which once set properly and minded, you should have no problems with running your GC analysis smoothly and without any issues.

Injector side – what sample, how much to inject and which liner to use?

First question to ask relates to your sample and if it contains volatile and thermally stable compounds. Only when the two above conditions are satisfied will you be able confidently to use the GC technique.

Commonly used GC injection techniques are liquid injection and headspace injection. The difference between the two is simple, if your compounds are very volatile and easily evaporated, I would recommend using headspace injection in which your compounds are evaporated in the vial and the cloud of gas is directly injected onto the GC column. Liquid injection takes a portion of liquid from vial, introduces it to inlet liner where the liquid is evaporated and moved from here to GC column for separation. Below we will mainly focus on liquid injection type.

What about your injection volume? Most analysts are using standard 1mL injection volume with 10mL syringes but there are also other, smaller syringe options available like 5mL and 1mL. It is very important to understand that injected liquid is immediately introduced to very high temperature and evaporated into gas cloud, therefore you need liner which has enough volume to handle your sample. It is enough to say that 1mL of water injected into GC creates 1414mL vapor cloud, 1mL of methanol creates 631mL of vapor cloud and 1mL of acetone  generates  347mL of vapor cloud, see https://uk.restek.com/solvent-expansion-calculator.

Very often we are neglecting the fact that there is a vast selection of different liners for different injection types, not always standard split liner or splitless will do the job. Additionally, when your liner is equipped with glass wool, the most important is the quantity of glass wool present in your liner and position of wool in the liner; this will directly affect results repeatability. When using liners with wool ensure not to exceed inlet temperature of 300°C, the liner wool usually deactivates at around 310-320°C.

Some examples of different liners are:

I always get the same question during GC training – how often do we need to change liner? Answer is not what you expect, I can’t tell you the exact interval. The frequency of liner change solely depends on your sample matrix; if you are performing liquid injection with only clean samples (like solvents) the liner will last for at least a year, on the other hand if your sample matrix is very dirty and you have no way of sample clarification, the liner might last as little as few injections. The most important thing is to periodically check the liner and septum to establish replacement frequency based on your own sample injections.

GC column(s)

Next, our sample enters GC column, and our job is to ensure that we have the correct column for the task, with no cracks, properly cut and mounted in our GC oven. Most GC systems on the market are designed for the column to fit perfectly into the injection port and detector requiring only hand tightening with a spanner and little force

When connecting a new column for the first time ensure to run the carrier gas through the column to remove any residual air and moisture from the column before you start injecting, at the same time ramp up the temperature of column. The reason is to replace the oxygen (O₂) on the column which can potentially oxidize liquid film layer, this is especially critical for polar GC columns.

Another important thing is potential thermal degradation on the column, with the temperature ramps your compound may elute at the wrong time onto the column where the temperature is too high for the compound itself and therefore causing some thermal degradation of your peak of interest. This can be prevented by lowering the ramp temperature or extending previous temperature ramp step. It is critical to know your compounds and related boiling points.

Unknown sample analysis – it would be a good idea to setup analysis using a neutral type of column; neutral columns exhibit higher temperature resistance allowing you to create higher temperature GC oven ramps

Other practical tips for column handling are:

• Column “baking” – set oven temperature to approx. 20°C less than maximum column temperature and let it run for at least 2-3 hrs, this will remove any moisture and air residuals from your column
• Column oven temperature starting point – approx. 10°C less than your solvent boiling point to allow better compound focusing, this should prevent broad peak at the start
• Column cooling rate – slower cooling rate must be employed for polar columns, too fast cooling will cause larger polar columns bleeding
• Practice column cutting before installation – use some old/disposable capillary column and practice column cutting to achieve straight cuts, you will perfect it in less than 10 cuts.

GC Detector(s)

After leaving the column our sample ends in the GC detector. I will point you to my previous blog, where we discussed in detail all possible and most common detectors in use with GC instruments.

Gas Chromatography Frequently Asked Questions

Can I inject water as sample matrix using liquid injection techniques into my GC system?

Yes, you can, but please mind the water expansion volume, also ensure you have the right column which can cope with water injections and resolve your compounds mixture to get a good chromatography. Best is to avoid water injections, but we all know it is not always possible.

I work with dirty samples, and I must change my liner after only 100 injections. Is it worth cleaning my liner(s)?

It is not recommended to clean or sonicate your liners. I always treat the liners as consumable and with the price of about 30-40 Euro a piece, I’d consider cleaning a waste of energy and resources. Just think about the time you spend cleaning the liner, electricity used for sonication and your GC system downtime before the liner is back in your GC inlet, all these are costs, and they most probably add up to be more than 40 Euro in total. Additionally, from practical point of view sonication can damage the liner’s deactivation, and scrubbing/cleaning can create scratches and introduce potential unwanted active sites on liner surface. Active sites on liner surface can cause peak tailing and poor reproducibility. All this can result in more trouble than you may expect and none of these should be of concern when it comes to brand new clean liner.

Can I replace, pack or re-pack glass wool in my liner?

It is not common practice to replace the glass wool in your liner, however some of us like to do it. I already explained the reasoning for replacing liner rather than cleaning it. When thinking of changing the liner glass wool ensure to reach out to your liner manufacturer and establish the exact amount of glass wool in liner you are using. It is critical to remember that incorrectly positioned glass wool or incorrect amount of the glass wool in liner will cause peak tailing or irreproducible peaks. Not to mention that you will most probably scratch the internal liner surface creating unwanted active sites.

My baseline is high, what can I do?

A high baseline will cause issues with peaks integration and potentially with sensitivity determination for your compounds of interest, especially those which elute towards the end of the run. Check a few things first:

• GC column conditioning – increase in baseline can be caused by incorrect column conditioning or “baking”, try to recondition the column
• Column contamination – check your gases for impurities or incorrect gas grade; check the gas line filters – maybe they need to be replaced; potential sample matrix buildup at the front of your column
• GC system leaks – small leak on the GC system can cause oxidation of your column stationary phase which causes column “bleeding” raising GC baseline; try to fix the leaks and if after fixing the leak(s) high baseline is still present maybe the column is old and it’s time to replace it.

My usual peak responses changed, what can I do?

Sometimes we find that our known peak responses change for no reason, right. Those unwanted peak response variations will affect detection limits, accuracy of quantitation and sensitivity. When this is the case watch out for below:

• Sample – check if the concentration is correct; verify if sample/standard preparation procedure did not change; check if sample/standard you used is within expiry date
• Syringe – see if there is air bubble/pocket in syringe, check for blockage, verify autosampler is working correctly
• Injection port – check the liner and septum, ensure injection port is “gas tight”
• Method settings – double check if the method settings for flow and temperature are used
• Leak(s) – ensure no leaks on the GC system
• Detector – double check the detector settings are correct, small change may have massive impact on peak response; verify that there is no contamination present

Peaks on my GC chromatogram are poorly resolved, why?

Sometimes we find that our peaks are not too well resolved, coeluting is least to say. This of course impacts both qualitative (identification) and quantitative results. When this occurs, you can have a look at the following:

• Issue with GC column stationary phase – potentially incorrect column type was selected for the job, and you need to change to a different, more suitable, column type for your compounds of interest
• Linear velocity issue – method you are using will need to be optimized, based on the type of carrier gas you are using there is always a “sweet spot” for best optimum resolution for Helium, Hydrogen and Nitrogen being used as carrier gas. Optimization may include both linear velocity and oven temperature program
• Sample overload – if you inject too much one thing you can expect is trouble; sometimes peaks will split and neighboring peaks will “suffer” the consequences; resolution will be lost between closely eluting peaks because of peaks getting broader. To resolve the issue – check sample/standard concentration, scale down injection volume, change to split method or increase the split ratio.

Gas Chromatography – Master the Basics

I hope that our last blog in 2025 will help you to use some simple fixes and guide you to correct solutions for your GC problems. I believe you appreciate that there is never a single answer pinpointing to single solution to your problem, but the above blog is dedicated to help you narrow down solutions and point you in right direction when solving GC issues.

Should you wish to discuss the GC technique and available GC instruments portfolio, please do not hesitate to contact me directly.