A GC Troubleshooter's Toolkit


LCGC North America

LCGC North AmericaLCGC North America-07-01-2012
Volume 30
Issue 7
Pages: 570–577

Many tools gas chromatographers keep on hand are specialized, but others can be found in the toolkits of plumbers and carpenters.

It has been about nine years since this list was last published in LCGC (1). During the interim, my toolbox has gained some new items, and a few others have seen little or no use. Given the modern obsession with list-making, readers may enjoy this update and perhaps learn about some tools they might like to add or replace in their own toolkits.

Every profession has its specialized tools. Those used in chromatography often are just as specialized as those used in computer repair or automotive work. Many of the tools and accessories that gas chromatographers keep on hand for installing, maintaining, and repairing their chromatographs are also found in the toolkits of plumbers, carpenters, and homeowners. Wrenches, screwdrivers, pliers, and metal-tubing cutters are some easily recognized examples. Other items such as dental instruments or paper correction fluid are familiar, but their use in the laboratory environment might not be immediately obvious. Still others, like a column flowmeter, septum nut wrench, or a specialized fused-silica column cutter, aren't found outside the laboratory at all.

Here, then, is the list of today's tools and accessories along with some information about their use and significance. One or more specialty manufacturers offer many of these chromatography-specific items in their catalogs or on-line offerings. I scanned through several catalogs and web sites and gleaned some new items that I have included here.

Butane Lighter

A butane lighter is a convenient source of hydrocarbon gas for measuring an approximate unretained peak time. Butane is effectively unretained at temperatures above 75 °C on liquid-phase coated columns with phase ratios above 50. Columns at low temperatures or with lower phase ratios (thick stationary films) may retain butane and separate the traces of ethane and propane present in the butane fuel. Use the earliest observable peak for the best estimate of unretained peak time. Natural gas is mostly methane; if your laboratory has a supply of natural gas (mine doesn't) it makes a good substitute for a lighter and is less retained than butane. Just be sure to turn off the gas after you've filled a syringe with it. A lecture bottle of methane with a suitable pressure regulator is another excellent source of the unretained substance. Concentrations in the low percent range work well.

Hydrocarbons won't work for unretained peak time measurements with electron-capture detection (ECD). Instead, try loading the syringe with a puff from a pressurized can of dust remover such as Dust-Off, which contains 100% 1,1-difluoroethane.

Hydrogen or helium — whichever is not the same as the carrier gas — make good unretained peak markers for porous polymer or molecular sieve columns that retain hydrocarbons strongly, plus these two gases should be readily available in most gas chromatography (GC) laboratories. Flame ionization detection (FID) will not respond to hydrogen or helium, but other detection methods such as thermal conductivity detection (TCD), pulsed discharge detection (PDD), or helium ionization detection (HID), the latter with hydrogen as the unretained substance, should respond well.

Cable, Three-Wire

Recorder cable finally has gone the way of chart recorders: You might find some lying around but they haven't been used in years. I have one or two in the lab just in case the need arises. I keep some spare USB cables as well.

Correction Fluid

Use white correction fluid to mark the measured position on a column that corresponds to the correct column penetration depth into an inlet or detector. Measure the depth after inserting the column into the nut and ferrule and making a fresh cut on the column end. Some regulated laboratories' policies don't permit the use of correction fluid for data integrity reasons. A septum into which a slot has been cut may be slid onto the column below the nut and ferrule to act as a positioning aid. Remove the septum before heating the column oven. A positioning gauge (see "Ruler" below) is a good alternative. I also have used a black permanent marker for this purpose; just be careful not to get it on your fingers or clothing.

Cutters, Fused-Silica Column

The best fused-silica column cutting tool is the one that holds the column in an adjustable chuck and cuts with a diamond chip as the operator rotates a thumb wheel. This tool also has a magnifying glass on the opposite end for inspecting the fresh cut for squareness and lack of burrs or hanging polyimide coating. A pen-like tool with a sapphire tip or ceramic scoring wafers or scribes that make a sharp cut on the column so that it may be broken cleanly in two are the best inexpensive alternatives. In any case, a fresh cut should be made and inspected just before placing the column into the inlet or detector and after sliding on the nut and ferrule.

Cutters, Tubing

A large plumber's tubing cutter for 1/4-in. metal tubing and a smaller one for 1/8-in. tubing are used extensively during instrument installation and gas-supply setup. The correct 1/8-in. size cutters are available from some chromatography supply companies — don't try to use the mini cutters found in home supply stores. Keep a supply of new cutter blades on hand. These disks wear out rapidly, and a dull blade will distort the tubing diameter and make it difficult to slide on the back and front ferrules. Power cutters with high-speed rotary abrasive cutting wheels are also available. These are mandatory for cutting 1/16-in. tubing for low-dead-volume gas valving applications, and they work well for any tubing up to 1/4-in. diameter. After cutting and squaring the tubing (see "Tubing Reamer" and "Deburring Tools" below) be sure to clean out the ends with a solvent such as isopropanol so that loose particles can't get into the instrument components or interfere with the passage of peaks through column ends.

Deactivated Fused-Silica Tubing

Gas chromatographers can use 5 or 10 m of deactivated 0.53-mm i.d. fused-silica tubing with a press-fit connector as a retention gap when necessary. Shorter pieces can act as a column-to-detector adapter when you don't want to put the coated column end into a detector to avoid column bleed from the column end at hot internal detector temperatures.

Dental Mirror

A plastic dental mirror with a front-silvered surface makes it easy to examine the underside of an inlet fitting in the oven, or to check other inaccessible areas for loose or missing parts. The mirror can also be used to detect the flame in a flame ionization or flame photometric detector by observing condensation of emitted water vapor on the cool mirror surface. A shiny wrench is a good substitute for the mirror in this case.

Dental Pick

A dental pick is very handy for removing septa from septum nuts and debris such as bits of graphite ferrule from fittings.

Diagonal Cutters

Diagonal cutters are used only for cutting electrical wires. They should not be used as a substitute for a tubing cutter. Don't even think about threatening your fused-silica column with one!

Eyedropper, Plastic

I have a box of these that is in frequent demand. I use them to place small drops of isopropanol onto fittings for leak checks. Some types have rough volume indications more like a pipette, and I have used them to make a crude dilution of qualitative test mixtures when accuracy wasn't required.

Ferrules, Capillary Column

A good assortment of graphite and graphite–Vespel capillary column ferrules is essential. Keep at least 10 of each inner diameter in the fitting sizes that match your instruments' oven fittings. In a pinch, graphite ferrules can be squeezed into sealing on smaller columns than they were designed for. It's always a good idea to install new ferrules with a new column; old ferrules can be reused on the same column if a seal can be made without over-tightening the fitting.

Ferrules, Metal Tubing

Ferrules for metal tubing are also essential. I used to prefer brass ferrules for copper and stainless-steel tubing, but nowadays I match the ferrule material to the tubing because some brass ferrules will bind to stainless steel upon tightening. Some instruments use 1/16-in. or 3/32-in. stainless tubing. This tubing is best connected using 1/8-in. graphite–Vespel reducing ferrules for 1/8-in. fittings, or 1/16-in. ferrules for the 1/16-in. tubing. Chromatographers should be aware of the potential for atmospheric oxygen contamination of the carrier gas from improperly installed supply tubing and ferrules. Even with the best filtration in place, a leak between the filters and the instrument will nullify the effect of the filters.

Files, Needle

An assortment of needle files can be used to pick out ferrules from fittings, remove burrs, and shape the ends of metal tubing before it is connected to a fitting. Don't forget to clean off all traces of metal before connecting.

Flexible Magnetic Pickup

A flexible 2-ft magnetic pickup comes in handy when you drop a small part inside the instrument. Another similar tool has a three-jawed "claw" operated by a plunger, and it will pick up nonmagnetic items.

Flowmeter, Electronic

An electronic flowmeter is an expensive investment, but I believe that it will pay for itself many times over with improved accuracy and precision over bargain-priced bubble flowmeters. I prefer the type of electronic meter that senses flow directly and that allows the operator to select the type of gas in use, such as air, helium, or hydrogen. The option to calculate split ratios from the measured split vent and column flows is a handy feature.

Flowmeters, Bubble

If you use bubble flowmeters, keep two sizes on hand. The large size is good for measuring FID air or inlet split vent flows up to several hundred milliliters per minute. The smaller size is better for packed-column or hydrogen flame-gas flows in the 10–50 mL/min range. Don't try to use a bubble flowmeter to measure capillary column flows below 10 mL/min. The carrier gas will diffuse out of the bubble and you will get a low reading. Measure the unretained peak time instead and calculate the flow rate from it. Note that this calculated flow rate or the rate displayed by electronic pressure control will only be as accurate as the column dimensions the operator uses. See an earlier "GC Connections" (2) for a detailed discussion.

Glass Wool Insertion and Removal Tool

This item is useful for those who must install glass wool in inlet liners, or for the hardy few who pack their own columns and use glass wool to hold in the packing. These days I find little use for it.

Inlet Liners

Inlet liners are often broken or chipped during installation or removal. They also can become contaminated with sample residue or may lose their deactivation if used for too long at high temperatures. Keep some spares on hand, both for packed inlets and for split or splitless injections. If you use deactivated liners, it is better to purchase them already deactivated than try to treat them yourself because of the chemical hazards and waste disposal problems this will create.

Inlet Liner Removal Tool

A tapered high-temperature silicone rubber tool on a metal holder does a good job of grabbing glass inlet liners and removing them without cracking or chipping the liner top. Most GC instrument manufacturers will supply specific tools and instructions for a particular inlet option.

Leak Detector, Electronic

An electronic leak detector is expensive, but it is indispensable for finding small leaks around hot fittings or inlets on which a liquid cannot be used (see "Leak-Checking Solution" below). The most sensitive type of leak detector uses a small pump to pull air from a probe through a thermal-conductivity cell. The presence of carrier gas or hydrogen changes the thermal conductivity and causes a change in the detector's readout compared to a reference air flow. Sensitivity for nitrogen carrier is limited. I also have a small handheld, battery-powered leak detector that has a series of light-emitting diodes which indicate the detected leak rate. This detector is great to carry around in a laboratory like mine with lots of instruments and little clear bench space.

Leak-Checking Solution

In my toolbox, the only acceptable leak-checking solution is a small bottle of pure isopropanol with an eyedropper. Other solutions may contain material that can leak into the gas-supply lines or columns and cause ghost peaks or other contamination.


A small magnifier is used to examine freshly-made column or tubing cuts for burrs or uneven edges.

Manufacturer-Specific Tools

For each GC system, there are always some specialized tools. These are used, for example, to open up a split–splitless inlet or to remove the inlet liner. Perhaps a special wrench is required for FID system flame jet replacement. Whatever the case, keep all such tools with their instrument: you will need them eventually. Some of the chromatography suppliers offer their own versions of these tools, which often are more useful than the freebie ones that come with the instruments. Several companies have toolkits for a specific popular instrument that is a must-have item for me.

Mini Flashlight

A flashlight is very handy for inspecting the interior of inlets and detectors for obstructions, as well as for illuminating the oven interior. I prefer the type with the bulb on a flexible gooseneck. No one yet has built a GC oven with a light that comes on when the door is opened.

Nuts, Capillary Column

There are several different styles of capillary column nuts that are used in the GC oven. My toolkit includes some of each type for my instruments. I never try to substitute one for another, even though the thread sizes are the same.

Nuts, Metal Tubing

Nuts for metal tubing are more standardized than capillary column nuts. Swaged fittings normally are used for outside tubing connections and often for internal connections as well. Keep an assortment of 1/4-in., 1/8-in., and 1/16-in. sizes on hand. Don't try to mix nuts and fittings from different manufacturers. I've picked one type and tried to purge all the others from my lab, so I don't have to peer at the small letters on each fitting to discern its type.

Nut Drivers

Handheld nut drivers are a useful addition, but I find that I use them more at home than in the laboratory.


An artists' paintbrush with handle is handy to clean out debris from small areas inside detectors or inlets. It can also apply leak-checking solution to fittings, although I don't recommend this practice because of potential contamination of the gas stream with the leak-checking solution.

Paper Clips

Jumbo-size paper clips with smooth sides are convenient for blocking off inlet or detector fittings for testing purposes. Unbend the clip and attach it to the fitting with a nut and 1-mm i.d. graphite-vespel ferrule. With the column connection blocked off, you can pressure-check an inlet. A detector check can be run in this manner without column influences on noise or stability.

Pin Vise and Drills

A small pin vise and a set of drills can be used in an emergency to drill out a used ferrule or to enlarge one that is too small to fit a column. Sometimes the small drills can help to remove a ferrule that is stuck in a fitting or to remove debris from inside fittings or tubing ends.


I keep some small needle-nose pliers, a pair of larger multigrip pliers, and one pair of locking pliers in my toolkit. The larger gripping pliers are useful for holding a straight length of 1/8- or 1/4-in. metal tubing while cutting it, although I take care not to grip the tubing anywhere near a location where a connection is to be made because the scratches from the pliers would make it impossible to get a good seal.

Press-Fit Connectors

Glass press-fit connectors make it easy to repair a broken column temporarily (until a replacement can be installed). These are available in many sizes to connect fused-silica tubing of the same or different diameter. They also connect a column with a retention gap. One manufacturer now offers a vacuum–melting device that makes near-perfect connections.

Pressure Gauge, Inlet

I have a conventional 0–60 psig pressure gauge with a syringe needle attached that I can insert into an inlet through the septum. Once in a while I need to check the inlet pressure this way, instead of relying on the instrument's gauges or electronic pressure readouts.


PTFE tape is used sparingly on tanks and interconnecting fittings where threads form the seal. Use two layers of tape, not more, and wrap them around the threads in the direction the nut tightens so that the tape will be drawn into the fitting instead of pushed out. PTFE tape should never be used in swage-type ferrule-sealed fittings, where it will only cause a leak, nor is it used at the high-pressure supply cylinder connection. Several types of this tape are available; be sure to select the right one.


A small metal ruler measures the correct column penetration depth into an inlet or detector. Don't use a plastic ruler, because it might melt in contact with heated inlets or detectors. For convenience, make marks on the ruler that correspond to the correct inlet and detector depths. Several manufacturers offer capillary column installation gauges with the appropriate markings.


A good sharp pair of scissors comes in handy for opening packages of ferrules, or for making paper stars out of waste paper that's waiting to be recycled while watching for peaks to be eluted. Scissors are not to be used to cut fused-silica columns (but you can believe that I've seen someone try it).

Screwdrivers, Phillips-Head

I found three Phillips-head screwdrivers in my toolkit: large, medium, and small. The small one is part of a set of jeweler's screwdrivers with rotating handles.

Screwdrivers, Slotted-Head

I also keep three slotted-head screwdrivers. The small one is useful for securing electrical connections to screw-type terminals. My set of jeweler's screwdrivers in a small plastic box have a knurled body and a separately-rotating knob that make it easy to turn the shaft with one hand. They haven't seen too much GC use, but they are good for tightening the frames of my eyeglasses.

Seals, Inlet

Many capillary inlets use an internal O-ring seal to isolate the incoming and exiting split flows. These seals are available in a variety of materials, including silicone, graphite, and high-temperature polymer. Worn seals will cause internal leakage and performance losses. Keep a good assortment on hand for each instrument. Some instruments use a metal seal and washer at the bottom of split–splitless inlets. For these, I prefer the deactivated seals available from at least one supplier. A seal with a Vespel seating surface for the inlet liner was recently made available, as well.


Spare septa are a requirement. Septa should be changed often. If you wait until retention times begin to drift upward then it's too late — a significant leak that will compromise results already has developed. Keep both normal-temperature range septa as well as some high-temperature ones on hand. I handle my septa — and all internal inlet parts — with tweezers or cotton gloves: a little bit of finger contamination can create a significant baseline bleed level.

Static Pad

A static pad is a grounded, conductive plastic sheet onto which it is safe to place electronic components that must be protected from damaging electrostatic discharge. Any circuit boards removed from an instrument should be placed on a grounded static pad, or in a static-proof bag.

Static Wrist Strap

A grounded static wrist strap prevents the technician from imparting a potentially harmful static discharge into instrumentation or components. Always wear one when working inside an instrument or removing components, and in all cases be quite sure that the instrument power has been removed while the instrument itself remains grounded.

Stopwatch, Digital

A digital stopwatch times bubbles in a bubble flowmeter, and also times an unretained peak. It's often more convenient to use a stopwatch when setting up an instrument than to operate the chromatography data system for each test injection. Select a stopwatch with readout to 0.01 s. Some GC systems include a stopwatch function on the display that includes flow, split ratio, and linear velocity calculations. These days I just use my smart phone's stopwatch and timer functions, and then its calculator to find flow rates or average linear velocities. Good phone applications are available with additional chromatography functions.


I keep two syringes for setup purposes. One 10-µL syringe is for injecting methane or butane to measure the unretained peak time and ascertain that the flame is lit and carrier gas is flowing. The other is for making liquid test-mixture injections as part of a column check-out. Sample syringes are kept separately.

Syringe-Cleaning Wires

Syringe cleaning wires may be used in an emergency to clear septum particles or other debris from syringe needles. I recommend discarding stubborn contaminated syringes; take steps to keep the syringe clean instead.

Test Mixtures

Column and detector test mixtures verify column performance and detector sensitivity. Keep a fresh vial of each type on hand. Column test mixtures are available for polar and nonpolar capillary columns, and there are test mixtures for each detector type. Some manufacturers provide a detector test mix that combines components for testing several different detectors. After they have been opened, test mixtures can be kept for a while in septum-sealed vials. Their lifetime is limited because of gradual evaporation. If you keep test mix in a vial, remove the vial cap rather than puncturing the septum when withdrawing liquid for injection. Some laboratories find it more convenient to keep dilute test mixtures on hand because these are more easily disposed of than the concentrated mixes. Many laboratories have their own qualification and validation standards, of course, but the manufacturer's mixtures allow easy comparison to the factory test results.

Tube Bender

I use this simple tool to make controlled bends of copper or stainless steel tubing for connecting the supply tanks to the filters and then to the back of the instrument. Tube benders come in sizes to fit standard tubing diameters.

Tube Reaming and Deburring Tools

These tools are used to remove burrs and irregularities from metal tubing after cutting. They are available for the standard tubing diameters, and I highly recommend using them to ensure leak-free connections.

Tubing, Plastic and Rubber

I keep several pieces of black and clear silicone rubber tubing on hand for connecting my flowmeter to column ends, split vents, and other flow sources. The narrower pieces of tubing fit inside the wider ones so that I can adapt the flowmeter fitting to a variety of connections. Of course, I never use plastic or rubber tubing for any gas at elevated pressure or for permanent supply or internal connections.

Tweezers and Hemostats

A pair of tweezers can hold small nuts or ferrules without risking contamination with skin oils or a burn from hot items. Some tweezers have a convenient locking feature that frees one hand for other tasks, as will a spring-loaded hemostat. Rubber tips help hold fragile capillary columns or inlet liners.

Vial Crimper

Vial crimpers attach aluminum crimp-top seals to autosampler vials. Several crimp-top sizes are commonly used for GC: 8 mm for 0.8-mL vials, 11 mm for 1.5- or 2.0-mL vials, and 20 mm for 5-mL and 20-mL vials. Hand crimpers are the least expensive, and some are available with interchangeable jaws that accommodate different vial sizes. Automated benchtop crimpers are less mobile, but the jaws can be interchanged quickly and they are best for laboratories with high sample throughput.

Vial Decapper

Vial decappers perform the opposite function of a crimper: They remove crimp-top seals from vials. Decappers come in the same sizes as the crimpers and resemble a pair of pliers. Some caution is required when using these so as not to break the neck of the vial. After the caps are removed, the contents may be properly disposed. Some laboratories reuse sample vials, but I recommend a fresh vial for each sample if at all possible.

Vial, Autosampler

I keep a spare autosampler vial to check for carrier gas flow during column installation. Fill the vial halfway with distilled water and then insert the column outlet after connecting to the inlet and turning on carrier gas pressure. The presence of bubbles shows positive carrier gas flow.

Wipes, Laboratory

I wet these with some isopropanol and then clean any debris or oil off the ends of capillary columns before inserting them into inlets or detectors. They also are handy for tipping a drop of test mix off a syringe needle, if disposed of properly. Paper towels don't work as well: They may leave fibers behind, and they could deposit a chemical residue.

Wire Brushes

Wire brushes can dislodge particles and debris from detector parts and some sealing surfaces. Be careful not to score polished metal surfaces, or damage ceramics. It is better to replace a severely dirty FID flame jet or collector than to clean it forcibly.

Wrenches, Hexagonal and Star

A full set of inch and metric hexagonal wrenches comes in handy when some minor disassembly is required.

Wrenches, Open-Ended

I have an assortment of open-ended wrenches in inch sizes as well as a metric set. I keep two or three with the following sizes: 1/4, 5/16, ⅜, 7/16, 1/2, and 9/16 in., as well as 11/16, 3/4, and 1 in., although these latter sizes are used only rarely. I apply two wrenches at once to prevent counter-rotation while tightening or loosening fittings.

Wrenches, Adjustable

I have one large 18-in.-long adjustable wrench that looks like it belongs in an automotive garage. This is used exclusively for attaching or removing pressure regulators on gas tanks. I also have a smaller 6-in. long adjustable wrench that I use occasionally if someone else has walked off with the exact open-ended wrench size I need.


Chromatographers, like all craftspeople, use a variety of tools to practice their craft. In a pinch, tools that are somewhat inappropriate can be used to make do, but the rapidity and ease with which the right tool gets the job done make it well worth the expense of obtaining what's needed.


(1) J.V. Hinshaw, LCGC North Am. 21(4), 356–361 (2003).

(2) J.V. Hinshaw, LCGC North Am. 30(3), 224–232 (2012).

John V. Hinshaw "GC Connections" editor John V. Hinshaw is a Senior Scientist at BPL Global, Ltd., in Hillsboro, Oregon, and a member of LCGC's editorial advisory board. Direct correspondence about this column to the author via e-mail: lcgcedit@lcgcmag.com.

John V. Hinshaw

Related Videos
Toby Astill | Image Credit: © Thermo Fisher Scientific