HomeGas Chromatography (GC) Prevent GC Inlet Problems BEFORE They Cost You Time and Money

Prevent GC Inlet Problems BEFORE They Cost You Time and Money

Katherine K. Stenerson, Michael D. Buchanan

Reporter US, Volume 27.3


Our Technical Service chemists help GC users solve problems that are often the direct result of overused septa or dirty injection port items. Many of these costly problems could be avoided. This article discusses how simple, routine preventative maintenance of the injection port can reduce the risk of chromatographic problems and instrument downtime.

Getting Started

Every laboratory should have a preventative maintenance schedule that is adhered to, allowing their GC systems to produce optimal chromatography, day-after-day, monthafter- month, and year-after-year. An example of a preventative maintenance schedule is shown in Table 1. A separate maintenance log book should be kept for each instrument, where all preventative maintenance is recorded.

Table 1.Example of a Preventative Maintenance Schedule

Prior to and during installation, always handle GC septa, inlet liners, liner o-rings, and inlet seals with clean, solventrinsed tweezers. Do not touch these items with bare hands (fi nger oil is a contaminant) or gloved hands (phthalate esters are contaminants). Additionally, be sure to follow your GC manufacturer’s installation instructions.

GC Septa

The GC septum should be routinely replaced to reduce the risk of leaks and septum particle contamination. In fact, if the instrument is in heavy use, change the septum daily. Repeated use of the same septum will result in increased coring, which may introduce a leak and/or result in septum fragments being deposited in the inlet liner. Septum fragments in the inlet liner may result in extra peaks being observed in the chromatogram. If using MS detection, the mass spectrum of an analyte could be corrupted with extra m/z, as shown in Figure 1.

GC Septa
Mass Spectrum: Septa Fragments in Inlet Liner

Figure 1.Mass Spectrum: Septa Fragments in Inlet Liner

Inlet Liners

GC users should routinely inspect and replace the inlet liner to remove contaminants and active sites from the sample path. Samples passing through the liner can contain components that do not volatilize, leaving behind residue. As residue accumulates on the liner, chromatography is affected by the adsorption of subsequent analytes. Adsorption results in poor peak shapes, and sometimes loss of peaks in the chromatogram. The inlet liner should be inspected regularly, if not daily, and replaced with a new, deactivated liner when necessary. Figure 2 shows how active sites in a dirty liner can affect results.

Inlet Liners
Chromatography Problems with a Dirty Liner

Figure 2.Chromatography Problems with a Dirty Liner

Liner O-rings

If your instrument uses an o-ring that seals near the top of the inlet liner, it should be replaced frequently, at least once for every five liner changes. An o-ring is deformed and flattened slightly when sealed into the GC inlet. If the flattening is too severe, it can affect the o-ring’s ability to form a proper seal. If the o-ring begins to crack, a leak may develop, compromising the split/splitless flow dynamics in the injection port.

Liner O-rings

Inlet Seals

Many instruments have an inlet seal, often gold-plated, that the inlet liner rests on. Similar to inlet liners, sample residue can also contaminate the inlet seal, forming active sites that result in analyte adsorption. Access to the inlet seal is not as easy as access to septa, inlet liners, or liner o-rings. From inside the GC oven, the column and a reducing nut must first be removed from the injection port. A thin washer that rests below the inlet seal should also be replaced. The inlet seal and washer should always be replaced when a new column is installed.

Inlet Seals

Injection Syringes

An often forgotten component that needs to be replaced periodically is the injection syringe. Over time, contamination may reside in the syringe barrel or in the needle, observed as extraneous peaks in the chromatography. Additionally, when performing manual injections, finger oil can be transferred to the plunger, causing it to stick inside the syringe barrel.

Split Liners

Problems can occur over time within the split lines of the injection port. Injection of sample volumes in excess of the liner capacity can result in flashback, which can contaminate the split line. This can then result in “ghost peaks” in subsequent chromatographic analyses. Septa particles and sample residues can build up in split lines and cause a plug, which will result in problems maintaining proper flow to the inlet. Finally, on some GC systems, to access the inlet liner, a large nut to which the split line is attached must be removed. Frequent manipulation of this nut can result in kinking and/or breakage of the split line.


While not injection port items, purifiers are mentioned in this article because they have a direct affect on the quality of the carrier gas entering the injection port. The three contaminants that need to be removed from a carrier gas stream are hydrocarbons, moisture, and oxygen. Using a multi-bed purifier that removes multiple contaminants, or several single-bed purifiers that each remove a separate contaminant, are both viable options. Replacement of purifiers when they become saturated will ensure a continuous supply of clean carrier gas into the injection port and GC system



GC users often overlook or disregard the importance of preventative maintenance, and only act when a problem is obvious. There are several important injection port components that require attention to reduce the risk of problems. These items should be checked and replaced regularly, particularly when installing a new column. Be proactive with your maintenance today, or be sorry with your results tomorrow.

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