The Gas Chromatographer’s Tool Kit

I suggest that you keep a fully stocked tool kit for each instrument; there is nothing more frustrating than needing a tool or supply item, going to the drawer, and not finding it. It is best to have everything you need available and ready when maintenance is needed. Tools and supplies for each zone: gas supply, inlet, column, oven, and detector are discussed.

The gas chromatographer’s tool kit begins with a toolbox. As the tools and supplies for maintaining a gas chromatograph are generally small, a large toolbox is not needed. The boxes or drawer organizers for small office supplies can serve this role quite well. I suggest a box with a snap-shut lid, so that your tools will not fall out if tilted or dropped, that can easily fit into a laboratory drawer. I keep mine in the bench drawer or cabinet under each instrument. Table 1 summarizes the tools and supplies discussed in this article.

Next, there are several general, non-specialized tools, the kind you can find at the local hardware store. Note that I will be mixing English and metric dimensions; this is one of the challenges of working in the United States!

Open-ended wrenches. A good set of open-ended wrenches, with wrench claws on both ends, not one end with a socket, is a must. Most often, you will need a 1/4 in. wrench for turning ferrule nuts and making other small tubing connections, and a 7/16 in. wrench for making larger tubing connections with 1/4 in. outside-diameter tubing and fittings. I keep a complete set of wrenches from 1/8 in. to 1 in. in the laboratory, with an extra 1/4 in. and 7/16 in. wrench in the toolbox for each instrument. For some of the common sizes like 1/4 in. and 7/16 in., you may need two for connecting fittings.

Large adjustable wrench. For changing gas cylinders and loosening and tightening the regulator connection to the cylinder, a large adjustable wrench, capable of opening from 1 to 2 in., is needed for connecting regulators to gas cylinders. Ideally, keep this wrench on a hook or near the cylinders. I cannot estimate the amount of time and frustration I have spent hunting for the “tank wrench.”

Dust-Off. A can of Dust-Off, or keyboard cleaner, can be used to detect leaks in a GC–MS system. Usually, in the tuning menu, you can set the system to continuously scan. Simply spray the Dust-Off onto each fitting, starting at the transfer line and working back toward the inlet and gas tanks. If, after allowing time for the sprayed compound to pass through the column, a signal is seen, you have found the leak.

Forceps or tweezers. A good pair of fine-tipped forceps or tweezers has several uses, including removing an old septum, O-ring and/or glass sleeve from the inlet, installing a new one (it is not good to contaminate these by handling with your fingers), handling small parts, especially in GC–MS ion source cleaning and maintenance, and recovering small parts dropped into inconvenient locations—this happens more often than you think.

Flashlight or headlamp. Often, you will be working inside the oven compartment, where lighting is not ideal, and the parts you are handling are small. A small flashlight is very helpful; I have started using a light-emitting diode (LED) headlamp to keep my hands free.

Magnifying glass. A jeweler’s loupe or your phone camera. You will need a strong magnifying glass to check your column cuts and ensure they are clean, square, and free of debris, such as ferrule pieces around the column end. If your phone camera has a strong zoom feature, this works, as well.

Your instrument’s maintenance guides and repair manuals. These are mostly online today, but should be readily accessible. Even though I have been working with gas chromatographs for over 30 years, I still refer to “the book” when it comes to repairs and troubleshooting. Many instrument and column vendors also publish troubleshooting guides online.¹

Several specialized tools and consumables are also needed. These are sorted into four categories: gas supply, inlet care, column care, and detector care.

Gas supply tools and parts. Gas supply manifolds often require occasional repairs as tanks are replaced and the tubing or fittings are moved or adjusted.

Replacement tubing, ferrules, and fittings. Be sure to have adequate tubing supplies, ferrules, and fittings for replacing any of the tubing between the cylinder and the instrument. The brass and stainless-steel fittings commonly used with gas supply tubing have a limited lifetime, especially if loosened and tightened often during maintenance procedures, and eventually may leak. Ensure you have spares on hand.

Electronic gas leak detector. This is one of the most important items in the laboratory, especially when working with hydrogen, which is flammable and can be a hazard with leaks, or helium, which is expensive. In any event, use the leak detector whenever a fitting is opened, after inlet, column, or detector maintenance, any time a fitting is opened, or if a leak is suspected. Remember to keep spare batteries and/or the charging cable in hand. Never use Snoop or other soap solutions on tubing for GC. The soap will irreparably contaminate the tubing.

Replacement scrubber cartridges or adsorbents. Have an adequate supply of replacement materials for scrubbers. These include replacement cartridges and adsorbents such as molecular sieves and indicating adsorbents. Be ready to replace these on a schedule or as needed. The one thing that is worse than no scrubber is an overloaded scrubber. This is a common source of elevated baselines and ghost peaks.

Tubing cutter and file. A small tubing cutter for copper and stainless-steel tubing will let you cut tubing to the proper length, ensuring tight connections. A file is then used to ensure circular openings at the ends of the cut tubing and to remove any burrs or imperfections at the ends that would prevent a tight, leak-free seal when connected. You should use your magnifying glass to confirm clean tubing cuts.

Electronic flow meter. Although today’s instruments have electronically controlled pneumatics and the data system automatically sets and records flows, it can still be useful to have a flow meter for troubleshooting and to confirm the flow rates reported by the data system.

Inlet and injector care. The inlet is the most complex part of the system, the most prone to contamination, and the area where you will be doing many of your maintenance activities. In capillary gas chromatography, the inlet must be kept scrupulously clean.

Septum puller. Many users prefer a specialized septum-pulling tool to tweezers. Usually, a septum puller has a small hook or curve on the end that can be used to pull a septum by engaging with the hole.

Septum nut and weldment wrench. Many of Agilent Technologies’ GCs include a specialized wrench for removing and tightening the septum nut and the weldment that allows access to the glass sleeve. Do not lose this.

Spare septa, o-rings, and inlet liners. Make sure to have a ready supply of septa (replaced every 30–50 injections), inlet liners (replaced as needed), and o-rings (always replaced along with the inlet liner). A few used septa can be saved for storing columns; otherwise, used septa, glass inlet liners, and O-rings should be discarded.

Spare gold seals and bottom fittings. Whenever the inlet liner is replaced, the bottom of the inlet should be inspected with a flashlight. If it is dirty, it may be possible to clean it with a cotton swab and a solvent such as methanol. If not, then it should be replaced.

Spare syringes and syringe cleaning wires. Have at least one spare syringe on hand, as your syringe will eventually wear out and leak, or the needle will be z-folded by the autosampler. Sometimes a syringe needle can be clogged with a piece of septum or other debris. A cleaning wire (this came with the syringe) can often clear the blockage.

Column care tools. There are several tools and supplies needed for proper column care and installation. As with the others, I would keep a complete set of these with each instrument, so you do not have to go hunting for them.

Ferrule setting jigs to the correct insertion distance. In the past, we set ferrules onto columns using a ruler to measure the correct length of column beyond the ferrule, marked the column at the bottom of the nut or fitting with correction fluid, then inserted the column into the inlet or detector. Seeing the white correction fluid ensured that the correct insertion distance was set. Today, there are various tools and jigs for setting ferrules to the correct position for each instrument. Keep these handy.

Used septa. Keep a few used septa available for storing columns after and between uses. If you change columns often, you may remove a column and want to store it for later use. The best way to do this is to keep the carrier gas flowing through the column as long as possible, then disconnect the column, and then poke the column ends into the old septa to seal them. This ensures an inert, mostly carrier gas atmosphere inside the column during storage. Remember that the column ends were sealed when purchased. They should be sealed when stored.

Ceramic scoring wafers. Whenever you change or install a capillary column, you will need to trim both column ends. This is best accomplished with a ceramic scoring wafer, available from all column vendors. Ensuring a proper column cut is critical to instrument performance and often is as much an art as a science. Your column vendor can point to instructions, or you can check out the videos in CHROMacademy, LCGC International’s online training platform.² There have been many tools used for scoring columns over the years; ceramic wafers are by far the best.

Spare columns. Have spares of your commonly used columns immediately available. Few things are more frustrating than having to order a new column when the existing column performance degrades. At least, monitor the performance of the existing column, and if it starts to degrade and trimming does not solve the problem, a new column is needed.

Detector care. The main challenge with detectors is keeping them clean; this is why the detectors on all gas chromatographs are heated, to prevent samples from condensing and fouling them. With use, detectors can become fouled in several ways. Each detector is unique, but there are several common tools and supplies to keep on hand.

Cleaning wires. Most detectors have a jet or opening through which the sample passes. If the jet becomes clogged, a narrow cleaning wire, like the ones used for unclogging syringe needles, can be used.

Detector-specific tools. Some detectors require specialized tools for disassembly and cleaning. These are generally shipped with the instrument or are available from the vendor. One example is the hexagonal socket driver that is used to remove the flame jet in flame ionization detectors from Agilent Technologies. Do not lose these or store them with the more common tools.

For GC–MS, lint-free nylon gloves and ion-source cleaning supplies, such as alumina powder, very fine-grit sandpaper, cotton swabs, cleaning solvents (as recommended by the manufacturer), and dedicated clean beakers for source cleaning.

For GC–MS, have spare filaments on hand. Filaments can die suddenly, like a light bulb burning out. All of a sudden, you have no signal. While most ion sources have a second filament, they still require replacement.

For older GC–MS systems. If your ion source has small screws and small ceramic spacers, have spares available. There are few things more frustrating than dropping or losing a screw and not having an immediate replacement.

Every gas chromatograph needs a tool kit to make routine maintenance and troubleshooting simple and convenient. I suggest that the tools discussed in this article be on hand for each instrument. That way, you will never encounter the extremely frustrating situation of needing a tool or small part and having to wait because someone “borrowed” the tool or used the last part.

References

1. Restek Corporation. GC Troubleshooting Basics. https://discover.restek.com/videos/gnav3593/gc-troubleshooting-basics (accessed May 2026).
2. ChromAcademy. http://www.chromacademy.com (accessed May 2026).