Do's and Don'ts

June 1, 2008
John V. Hnshaw
LCGC Europe

Volume 21, Issue 6

Page Number: 332–337

Successful gas chromatography (GC), akin to many other disciplines, requires regular attention to a number of routine procedures. Chromatographers, similar to anyone else, develop habits in their daily work. Some of these help create a successful laboratory environment, while others can be ineffective or worse, can create more problems than they solve. This month, "GC Connections" presents a few of the best and worse laboratory habits.

One of the most critical areas for obtaining the best results is instrument installation and set-up. Without the right equipment and supplies, chromatographers run the risk of compromizing an instrument's potential to deliver the required level of performance. Here are some important do's and don'ts for installation and set-up.

Do Obtain a Preinstallation Checklist From the Instrument Manufacturer and Follow It

Instrument manufacturers are the best source of information about installation requirements. Following such guides is a very good habit to acquire. Detailed lists of the correct supplies and services that an instrument will require are readily available. For example, the electrical supply must be of the correct voltage and frequency, it must be properly grounded and it might require an individual connection and circuit breaker. Additional considerations. such as power filtering, surge suppressors and uninterruptible power supplies (UPSs), are important for the data handling system associated with an instrument. Also, the laboratory temperature and humidity should fall within specified guidelines. An approximate British thermal unit (Btu) output rating for an instrument helps estimate the load on laboratory air-conditioning systems. Sometimes adding a number of new gas chromatographs requires an upgrade to existing heating, ventilating and air conditioning (HVAC) systems.

Do Pay Attention to Gas Delivery Requirements

The types of gases that the instrument requires depend upon the installed inlets and detectors. Capillary inlets and trace-level detectors need higher-grade gases than packed inlets or thermal conductivity detectors. The installation checklist will specify additional items such as tubing, filters and basic supplies. Appropriate gas supplies should be on-hand before an instrument arrives in the laboratory.

Many preinstallation checklists provide detailed plumbing diagrams for commonly configured combinations of inlets and detectors. Another good source of this information is available in Bulletin 898, "Gas Management Systems for GC", from Supelco (Bellefonte, Pennsylvania, USA). This publication includes a wealth of general information on gas chromatograph installation as well as detailed diagrams of appropriate connections for many combinations of pneumatic components. It covers tanks, gas generators, regulators, tubing, on–off valves, fittings, multi-tank manifolds, gas filtering, leak detection and multi-instrument installations. The brochure also contains ordering information for many recommended components.

Don't Wrap Gas Fittings with Lots of Pipe-Sealing Tape

The logic behind this practice is that more is better. I have seen white tape where it will do no good, on high-pressure tank fitting threads that do not provide a seal in the first place, as well as on the nipple-and-cup sealing surfaces where the tape is more probable to cause a leak than prevent one. Sometimes sealing tape even shows up wrapped around the ferrules of 1/4 or 1/8 in. swaged tubing fittings. The correct application of sealing tape is two layers applied to the threaded portion of pipe or tapered fittings before assembly. Remove all old tape and residue beforehand, and do not over-tighten: one-half to one turn beyond finger tight is all that is required. Wrap the tape in a direction so that it doesn't unravel when the fitting is screwed-in. Never apply tape to swaged or compression fittings. Instead, use new ferrules when required.

Do Use the Correct Grade of Carrier and Detector Gas

Good, clean supplies of carrier and detector gases are well worth the expense. Get into the habit of using the right gas grade from a reliable source as the first requirement for establishing the best supply. Be sure that your gases are manufactured specifically for GC use. Select the gas grades specified by the instrument manufacturer for the exact inlet, column and detector. Although a lower grade might work, you risk encountering problems later on as contaminants accumulate or the column degrades more rapidly than it should.

Gas generators are an attractive alternative to tanks as air and hydrogen sources. The rising cost of helium carrier gas is making the switch to hydrogen more and more attractive: the cost of a high-purity hydrogen generator can be recovered after producing the equivalent of as few as eight tanks. Gas generator delivery capacities are limited, though. One generator will support a limited number of instruments, so be sure to determine in advance the total flow requirements from the number of carrier channels and detectors in use.

Do Install High-Grade Pressure Regulators

It would be a shame to purchase expensive gases or gas generators only to contaminate their pristine output by using inexpensive pressure regulators and other less than top-grade gas-delivery devices. Those old single-stage cylinder gas regulators belong in the welding shop or party balloon store and not in the laboratory. Develop a habit of using only high-purity dual-stage regulators rated for GC. These devices wet the gas stream with noncontaminating material and they incorporate high-quality seals that prevent the influx of atmospheric oxygen. In the improbable event of failure, most high-purity regulators include a safety vent that will direct the high-pressure gas to the atmosphere and not into the GC system.

Don't Vent the Gas Tank's High- Pressure Outlet Before connecting a Gas Regulator

Myth: Venting high pressure tank gas to remove dirt particles from a tank's outlet fitting is required to obtain a good seal and keep dirt out of the pressure regulator. I've encountered this practice while visiting several different laboratories. The telltale roar of helium gas escaping at 2400 psi always startles me. The particles would seem to be a leak source if they end up on the tank fitting sealing surfaces; they also might enter the regulator and interfere with its operation. However, gas manufacturers ship high-purity GC gas tanks with a plastic cap on the tank fitting that keeps the dirt out in shipment and storage. And quality dual-stage GC gas regulators include a sintered metal frit in the entrance that stops any particles from entering the regulator. In fact, venting a high-pressure gas tank is potentially dangerous because of uncontrolled pressure release: the gas stream exits from the tank valve with a force exceeding one ton per square inch, strong enough to cause extremely serious injuries.

Do Use a Purge-Tee Fitting Downstream From the Regulator

It is necessary to vent a gas system upon installing a new tank; some air incursion into the lines will always occur. The best way to keep air away from active filters and the gas chromatograph itself is to install a purge tee with restrictor in-line. Then, after reconnecting the pressure regulator at the tank and turning on the tank pressure, open the purge valve and the regulator shut-off valve for one minute or so. This will vent the initial gas output away from the devices downstream. I once connected a helium line to a gas-sampling valve in a GC system with a molecular sieve column, as part of another experiment; I was surprised at how much gas is required to bring the air contamination down to under 50 ppm after disconnecting and reconnecting the regulator.

Don't Check Newly Attached Gas Fittings for Leaks With a Liberal Application of Soap Solution

This one should be left to the plumbers and refrigerator service people. Almost every GC laboratory seems to have several bottles of soap solution with a paintbrush or dropper that enforces a liberal application. The problem is that a leak is a two-way street: gas goes out but soap, as well as atmospheric oxygen, can go in. Once inside, the water evaporates and leaves a soap film behind. If applied directly to pressure regulators and needle valves, the soap residue will interfere with their operation. Surprisingly, some soap solutions contain organic surfactants that have significant vapour pressures and can migrate along the gas lines into inlets and detectors. It doesn't take much: many GC detectors respond to sub-part-per-million levels of organics. Use isopropanol instead of soap solution, or better, acquire an electronic leak-checking device.

Do Install High Performance Gas Filters

Having just spent a substantial sum on high-quality gases and pressure regulators or on a gas generator, you will want to develop the habit of installing the best gas filters to maintain gas quality on its way into your GC system. Although filtering high-purity gases might seem redundant, in reality it is not. There are a number of unions in any gas supply set-up, each of which is a potential leak. The number of connections and, therefore, the chance for a leak, increases in proportion to the number of instruments in use. Gas-line tubing also presents a potential contamination source, especially if the tubing is reused by migration from one instrument set-up to another. I once saw a laboratory with manifolded carrier gas supplies where they had done everything correctly, except for the cheap on–off toggle valves at each instrument; they risked contaminating the carrier with air at the last moment before going into the instrument.

Ensure the best possible gas purity by placing a series of filters as close as

possible to the instrument. Solely putting filters in-line immediately after the gas cylinders does not help as much, especially if multiple instruments are connected to a single group of tanks. Some laboratories put high-capacity filters next to the tanks and include "final" filters at the instrument bulkheads.

Select high-performance filters, and then change or regenerate them regularly. Replenishing filters after a few tanks worth of gas is good practice. For carrier-gas supplies, use a molecular sieve filter, then a large-capacity oxygen trap and finally an indicating oxygen trap. Some analysts include a charcoal trap just before the molecular sieve trap. For detector supplies, a molecular sieve filter and possibly a charcoal trap are desirable — you will need an oxygen filter for an electron capture detector. Avoid using inexpensive moisture traps, as the adsorbent material might not remove all of the water. There are some very good combination filters and filter manifolds available that include built-in isolation valves for ease of filter element replacement.


Periodic maintenance often gets neglected because instrument operators haven't set aside the time to perform such tasks regularly and are saving their energy for heroics when something does go wrong. It's far better to assume that there will be a problem at some point, and then take precautions that will delay or minimize the eventual difficulties. Here are a few of the more often-overlooked trouble spots.

Do Use a New Ferrule Whenever Connecting a Column

The column–ferrule–fitting link is one of the weakest and most-often compromised connections in a GC pneumatic system. While reusing ferrules a few times is a tempting cost-saving habit, it's a very good idea to use a new ferrule whenever connecting capillary or packed glass columns to the inlet or detector. Although reusing a ferrule will often succeed, you risk the possibility of a leaking or contaminated connection. The exception is metal-packed columns with metal ferrules — they are not removable once in place, so be extra careful not to overtighten them.

Often, chromatographers remove a capillary column from the instrument and store it on the shelf or in a box. A common habit calls for sealing the column ends to avoid contamination or degradation of the stationary phase, often by inserting the column ends into a piece of septum. This is good practice, but it immediately contaminates the column with septum particles. Upon reinstallation it's necessary to trim off 1 cm or more from the column end to remove them. Flame-sealed column ends require trimming as well, by as much as one full turn. In either instance, once the ends have been trimmed it's necessary to reposition the ferrule so that the column rests the correct distance into the inlet or detector. This motion disturbs the seal between the ferrule and column surfaces; the seal cannot be reliably reestablished by tightening the fitting nut.

Do Inspect and Change Autosampler Syringes Often

An autosampler syringe is subject to far more actuations than a manually operated syringe. Autosamplers relentlessly move the syringe plunger through preinjection sample washes, sample acquisition and postinjection solvent washes. An autosampler syringe can experience 20 or more plunger actuations per injected sample. The presence of any non-volatile or particulate residue in the sample will greatly exacerbate the eventual demise of the syringe through plunger wear, plugging and residue build-up.

You can avoid, or at least delay, these problems by making a habit of taking several precautions. First, inspect and test the syringe every 100 samples, or when adding a full sample tray. Remove the syringe from the sampler and manually actuate the plunger with the needle immersed in an appropriate solvent. The plunger should move up and down smoothly. You should observe liquid move up into the syringe and see it squirt out of the needle. Check the needle and plunger for straightness. Carefully pull the syringe tip back over a clean piece of paper; any roughness or noticeable drag on the paper indicates the presence of burrs. Replace the syringe at the first sign of problems. The relatively small expense of a new syringe does not compare to the cost of lost samples.

Do Change Septa Regularly

Inlet septa are a weak spot in a gas chromatograph's pneumatic system. The syringe needle punctures the septum repeatedly and gradually punches out a small void that eventually extends straight through the septum to the pressurized carrier gas inside. But long before catastrophic failure, the septum will leak enough — especially in the first few seconds after injection — to produce a significant response with an electronic leak detector. This kind of acute leak self-heals quickly at first, but older septa take longer to reseal than new ones. Operation at higher pressures and inlet temperatures also reduces septum life.

Different types of septa are appropriate for different conditions and analyses. For routine packed column analysis, low-cost Teflon backed septa with a relatively soft silicone body work well. At higher temperatures, or for trace-level capillary work, high-temperature low-bleed septa are a necessity. The syringe needle pushes septum particles onto the inlet liner with each injection and these particles release volatile components directly into the carrier-gas stream. Pieces of high-temperature septa produce less background interference than other varieties. They are harder than the low-temperature septa, however, and may leak after fewer injections or at lower inlet pressures.

Do Inspect and Change Inlet Liners Frequently

As a corollary to septum inspection, analysts also should pay close attention to the inlet liner. Any kind of contamination in the liner can have a dramatic effect on the chromatogram. Particles of dirt can cause peak tailing or even produce total adsorption. High-boiling sample residue can delay solute transfer into the column and produce peak tailing as well as solute loss with splitless sampling. Pieces of septum will bleed and introduce ghost peaks or silicone background peaks into the detector. Sometimes, syringe needle movement or large flow fluctuations gradually displace the liner packing downward, until the misplaced packing affects sample transfer from inlet to column. Periodic liner inspection identifies all of these problems.

Because pulling out the liner requires inlet cooling and depressurization, it makes sense to check the inlet liner whenever inspecting or changing the septum. Handle the liner with contamination-free gloves, because any contamination will be exposed to the carrier gas at the inlet temperature. Be sure to check the internal liner seal as well. After installing a liner, allow the inlet system and column to purge with carrier gas for at least five minutes worth of flow, while making sure that the column has been purged for at least five times the unretained peak time. Otherwise you risk ruining a column by heating in the presence of residual air.


Each GC system operates under a rule of cause and effect. Instrument performance depends directly upon the establishment of appropriate operating procedures, all of which combine to enhance day-to-day results quality. The list of good habits enumerated in this article represents a selection of some of the best procedures applied in a laboratory environment. Conversely, the "don't do this" items show how easy it is for chromatographers to go awry of good practices. Every step in installing, operating and maintaining a gas chromatograph should be subject to critical examination.

"GC Connections" editor John V. Hinshaw is senior staff engineer at Serveron Corp., Hillsboro, Oregon, USA and a member of the Editorial Advisory Board of LCGC Europe. Direct correspondence about this column to "GC Connections", LCGC Europe, Advanstar House, Park West, Sealand Road, Chester CH1 4RN, UK, e-mail:

For an ongoing discussion of GC issues with John Hinshaw and other chromatographers, visit the Chromatography Forum discussion group at