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Leak-Free GC

Maintaining a leak-free GC or GC-MS system is critical for obtaining optimal system performance with reliable, reproducible, and accurate results.

by Ken Lynam
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Tools, Supplies, and Best Practices for Improved Performance of Your GC or GC-MS Systems

This article discusses symptoms and problems typically observed because of leaks, how to identify leaks and correct them, and how to set up the system to avoid or minimize leaks. Topics include the use of high quality carrier gas, selection of the proper ferrule, proper just-tight-enough ferrule installation, how to check for leaks in GC and GC-MS systems, and making sure all column connections work together to create a leak-free environment.

Large leaks and small leaks

GC gas leaks fall into two distinct categories: large leaks that prevent the instrument from functioning and smaller leaks that allow the system to operate, but negatively impact chromatography.

Large leaks typically prevent a system from reaching a ready state, leading to an electronic pressure control (EPC) safety shutdown on equipped systems. These types of leaks can result if a column is not installed in the expected inlet or is not connected to the expected detector. Broken columns, broken or loose fittings, broken ferrules, cored septa, or blocked tubing are also possibilities. Visual inspection or review of the method settings will quickly identify the cause of major leaks.

Figure 1. US EPA 8081 pesticides before and after exposure to 1,000 μL/L oxygen in helium.However, identifying smaller leaks, which allow the system to continue to operate, can be more difficult. Symptoms of smaller leaks include continuous pressure cycling (oscillations greater than 0.02 psi), poor retention time reproducibility, higher than typical background, higher than typical bleed (particularly at temperatures above 230°C), baseline drift, higher than usual inlet activity, tailing peaks, the need for more frequent inlet maintenance, and poor area reproducibility.

An example of a minor leak is illustrated in Figure 1, which shows the elution of US EPA 8081 pesticides on a DB-1701 phase before and after exposure to 1,000 μL/L oxygen in helium carrier gas. After just 10 injections, column bleed increased significantly and a shift to shorter peak retention times was apparent.

Carrier gas considerations

High quality carrier and detector gases of known purity are essential. Use carrier and detector gas of at least 99.9995% (5.5 nines) purity, and zero-grade air for flame detectors.1 Inline indicating gas traps will remove hydrocarbons, moisture, and oxygen and ensure continued quality. Gas certification testing and product descriptions vary by supplier and so obtaining a certificate of analysis (COA) for your gases is essential to understand gas quality. On the COA, look for evidence of the tests conducted, contaminant specification, and indications of whether testing was done on individual (preferred) or representative cylinders from a batch.

Choosing the right ferrules

Selecting an appropriate capillary column ferrule for the column tubing size and its fittings is also critical to minimize leaks and keep the flow path free of contamination. One-size ferrules are used for 0.1 to 0.25 mm ID columns, while 0.32 mm and 0.53 mm ID columns each require ferrules with larger diameter holes to accommodate the wider outside diameter of these columns.

Ferrule material choice is also important for specific applications. Graphite ferrules are popular for general purpose and high-temperature applications (above 350°C) but, typically, are not as contaminant-free as polyimide/graphite or metal ferrules. Further, graphite is a porous material and slightly permeable to gases, creating a very small continuous leak, making graphite ferrules incompatible with oxygen-sensitive stationary phases or detectors such as ECD or MSD. Graphite also has a tendency to flake and extrude into fittings if overtightened, becoming a source of contamination and chromatographic problems like peak tailing.

Pure polyimide ferrules have limited use in GC, as they shrink dramatically when exposed to heat cycling. Polyimide/ graphite blended ferrules are the choice for GC/MS and trace level analysis with ECD. Unfortunately, they also have a tendency to shrink with repeated heat cycles, forcing you to snug the fitting repeatedly to fix leaks. Because ferrules shrink, the tendency is to overtighten fittings that use polyimide/graphite ferrules. Table 1 identifies some common attributes of ferrules for capillary columns.

Table 1. Ferrule characteristics
Requirement Graphite Polyimide / Graphite Flexible Metal
Low Torque needed; compatible with finger tight nuts  X  X  
Price X    
Re-use X    
Will not fragment   X X
Inert     X
Leak-free   X* X
High temp, above 350°C X    
MS interface   X  
CFT device    
Pre-swage for precise height in fitting    
*When using self-tightening column nuts avoid over-tightening

Don’t tighten more than you need

Overtightening can break the column or permanently damage fittings and produce leaks. Overtightening of hard, metal ferrules such as Swagelok®, SilTite™, or UltiMetal Plus Flexible Metal ferrules can damage fitting threads, making it impossible to obtain a seal and resulting in costly instrument repairs. Carefully read and follow the manufacturer’s instructions on fitting installation and use, to avoid chronic leaks from damaged fittings.

Proper installation of graphite or polyimide/graphite ferrules, inlet seals, O-rings, and septa is also critical to maintaining leak-free connections. Just-tight-enough (JTE) is the goal for proper installation of these somewhat pliable components. Tight is good but tighter is not better, as these pliable materials easily crush beyond their design specifications, causing them to leak sooner and more often. Overtightening fittings can cause failures such as peak tailing, line blockage, and column breakage. In extreme cases, with repeated overtightening of brass mass spec transfer line nuts, the nuts themselves could crack and potentially cause permanent damage to the mass transfer line.

Some septum nuts have a C-shaped clip at the top, so do not turn this type of nut more than three-quarters of a turn past where it begins turning with the nut assembly when a septum is being installed. Overtightening of the septum nut will cause premature septum coring with repeated injections, which in turn causes the septum to leak during a run. The septum nut is another fitting that needs to be JTE.

Checking GC connections

Checking all fittings for leaks immediately after installation, maintenance, and periodically while in use is an excellent practice. Handheld leak detectors are particularly useful for finding leaks quickly either inside or outside the GC oven. It is always good practice to use a leak detector every time a column, fitting, or cylinder is changed. An excellent starting point for system troubleshooting is to first check for potential leaks. However, avoid using water-soap solutions, as these can be drawn back into the GC flow path, severely affecting results or even causing permanent column damage.

Checking a GC-MS for leaks

A vacuum gauge is very useful for isolating potential leaks to either the vacuum (MS) or pressurized (GC) side of the instrument. Vacuum readings around 10–5 or 10–6 Torr are typical for a system that holds a vacuum with a flow rate of 1 mL/min on a 30 m × 0.25 mm, 0.25 μm column. When the MSD is capped and pumped down, vacuum readings typically drop to 10–6 or 10–7 Torr in the absence of a leak. A vacuum pump that does not reach these levels relatively quickly indicates a leak somewhere in the MS. Make sure the purge vent is closed, the transfer line fitting is installed correctly, and that the large O-ring on the vacuum side plate is also correctly positioned.

A software-based performance check of air and water could be available under the tuning selection tab. This check looks at GC-MS ion traces of molecules typically found in air relative to ion 69 in the calibrant. Ions 18 (water), 28 (N2), 32 (O2), 44 (CO2), and 69 (typical base peak from PFTBA used during auto-tune) are all monitored. Nitrogen levels above 10% relative to the 69 peak indicate that the system has not had sufficient time to pump down or that there is an air leak. An air leak will typically show nitrogen:oxygen at 4:1. Water is also typically present, particularly after a system has been vented and exposed to ambient air. An equilibrated leak-free system should show nitrogen well below 10%, with oxygen at about a quarter of the nitrogen signal, and ideally water lower than the N2 peak.

Troubleshooting leaks in GC-MS is a process of elimination, looking at every site where a leak can occur. A spray can of fluorocarbon (for example, 1,1,1,2-tetrafluoroethane, ions 69 and 83) or argon (ion 40), with a plastic tube to direct the flow, is very useful in isolating a leak. A short spray at a suspect point and monitoring the appropriate ions in manual tune is a powerful tool for isolating a leak.

Key points to check are the transfer line connection in the oven, septum nut, column nut, and the large O-ring on the vacuum plate of the MS. Once a leak has been identified you can fix the leak by replacing a septum, resetting a column connection, or cleaning the O-ring on the vacuum plate and reinstalling it back into the groove on the plate.2

Innovations to minimize leaks

Figure 2. Example of an air and water check. Figure 3. Self Tightening column nuts installed at the transfer line and inlet fittings.

Figure 2 shows a total ion chromatogram for an air and water check on a system that is operating normally. In this case, Self Tightening column nuts were installed at the transfer line and inlet fittings. These novel column nuts provide a leak-free seal when using a short polyimide/graphite blend ferrule at both column connections, without the need to retighten the fitting after more than 300 heat cycles.3 Use of these column nuts eliminates the need to retighten the inlet or mass spec transfer line connections after oven heat cycling. Furthermore, because very low torque is needed to make a leak-free seal, these nuts are installed using only fingers, not wrenches, which eliminates the risk of overtightening and damage to the fittings. (Figure 3).


By using tools, supplies, and best practices that provide a leak-free GC or GC/MS, you can improve performance and productivity of your system. New types of ferrules provide robust leak-free column connections, along with inert surfaces for fittings in the sample flow path. Innovative Self Tightening column nuts using standard short polyimide/graphite ferrules eliminate the need to retighten GC column fittings. Nonetheless, whatever types of fittings you use, the best option is to adjust fittings, septa, and O-ring seals to be just tight enough, and no tighter.


1. Anon. Agilent 7890 Series GC Site Preparation Checklist, Revision 1.6. Agilent Technologies, Inc. Publication number G343090001 (2013).

2. Anon. The right connections make all the difference. Brochure, Agilent Technologies, Inc. Publication number 59913155EN (2014).

3. K. Lynam. Proof of Long-Term, Leak-Free Performance for a Novel Self Tightening GC Column Nut. Application note, Agilent Technologies, Inc. Publication number 59913612EN (2013).