Troubleshooting and maintenance of GC Systems

Troubleshooting a GC chromatograph can be made easier, if one learns to recognize the symptoms produced by an instrument malfunction, column and detector problems, leaks. Many symptoms appear as unusual peaks as shown below:

Symptom: No peaks (Fig. 1) 

Fig. 1: No peaks appear after the injection of the sample
Fig. 1: No peaks appear after the injection of the sample

Possible Cause: Main power off, fuse burned out
Action: Plug in the instrument, replace fuse

Possible Cause: Detector off
Action: Turn detector on and adjust its sensitivity

Possible Cause: No carrier gas flow
Action: Check the carrier gas lines and correct the problem i.e. replace empty gas cylinders, possible obstructed or broken gas lines

Possible Cause: Injector temperature too low. The sample is not vaporized
Action: Increase injector temperature.

Possible Cause: Injector septum is leaking
Action: Replace the septum.

Possible Cause: The syringe used for the injection of sample is plugged up.
Action: Clean the syringe or replace it if it is damaged.

Possible Cause: The FID flame is out.
Action: Check the FID flame. Check if water vapor condenses on mirror. Light up the flame if needed.

Possible Cause: Column connections are loose.
Action: Check for leaks. Use a leak detector. If needed tighten column connections

Possible Cause: Oven temperature too cold. Possibly, the sample condenses in the column
Action: Increase oven temperature


Symptom: Retention times or areas are not reproducible (Fig. 2)

Possible Cause: Septum is leaking
Action: Replace the septum if it is damaged. If there is a premature septum failure (less than 200 injections) check also if:
The syringe needle is not straight
The syringe is not installed correctly
The septum retainer nut is too tight

Possible Cause: Syringe is dirty or damaged
Action: Replace the syringe if it is damaged. Clean the syringe with an appropriate solvent if it is dirty.

Possible Cause: Sample is not stable under the conditions of the analysis
Action: Check the sample stabiblity. Some samples change with heat or U.V. light. In case the sample is photosensitive use amber sample vials.

Possible Cause: Sample volume is too low or too high
Action: Check the sample vials. If the sample vials are not filled correctly, evaporation or contamination may affect the analysis. The sample level should be approximately half the volume of the vial.

Fig. 2: Retention times or areas are not reproducible

Fig. 2: Retention times or areas are not reproducible

Symptom: Poor sensitivity with normal retention time

Fig. 3: Poor sensitivity with normal retention times
Fig. 3: Poor sensitivity with normal retention times
 Possible Cause: Insufficient sample size

Action: Increase sample size. Check syringe needle for plugging.

Possible Cause: Poor sample injection technique
Action: Check if the proper injection technique is used.

Possible Cause: High attenuation
Action: Reduce attenuation.

Possible Cause: FID response low
Action: Optimize the flow rates of H2 and air. Use N2 for make-up gas

Possible Cause: Thermal conductivity response low
Action: Use higher filament current.

Possible Cause: Syringe or septum leaking when injecting
Action: Replace syringe and/or septum

Symptom: Poor sensitivity with increased retention time and broadening of the peak

Possible Cause: Carrier gas flow rate too low.
Action: Increase carrier gas flow.

Possible Cause: Septum is leaking.
Action: Replace septum.


Symptom: Irregular baseline drift (isothermal)

Fig.4: Irregular baseline drift when operating isothermally
Fig.4: Irregular baseline drift when operating isothermally

Possible Cause: The instrument location is not according to the manufacturer’s specifications .
Action: Instrument should not be placed directly under heater or air conditioner or any other place where it is subject to excessive drafts and ambient temperature changes.

Possible Cause: Column packing bleeding.
Action: Let column to stabilize as described by the manufacturer.

Possible Cause: Carrier gas leaking.
Action: Locate leaks and correct.

Possible Cause: Carrier gas regulators do not work properly.
Action: Check carrier gas regulators and flow controllers.

Possible Cause: Poor air or H2 regulation (FID detectors)
Action: Check regulators and flow controllers.

Possible Cause: Detector is contaminated
Action: Clean detector according to manufacturer’s specifications. Raise temperature and bake out detector overnight.

Possible Cause: Detector filaments are defective (TCD detector only)
Action: Change the filaments.

Symptom: Contamination or ghost peaks

Possible Cause: Vial cap septum is dissolving in solvent

Action: Check the vial septum. If it is not resistant enough to the solvent you are using try a more resistant type.

Possible Cause: Injection port septum is giving off volatiles
Action: Make several blank runs with a small piece of aluminum foil backing the inlet septum. If the contamination peaks disappear, they were probably due to the septum. Use another type of septum that is stable to the required injector temperatures.

Possible Cause: Column is contaminated
Action: Examine the first 10 cm of the capillary column for contamination holding a light behind it. If possible cut the contaminated part of the column. Replace or clean the inlet liner.

Possible Cause: The sample is not stable
Action: Store the sample in a protected environment and use amber sample vials.

Symptom: Sinusoidal baseline drift

Fig.5: Sinusoidal baseline drift
Fig.5: Sinusoidal baseline drift

Possible Cause: Oven temperature defective
Action: Replace the oven temperature sensing probe .

Possible Cause: Oven temperature control was set to a low value
Set the oven temperature control to a higher value.

Possible Cause: Carrier gas flow regulator defective
Replace the carrier gas flow regulator. Set to a higher pressure in order to stabilize the gas flow.

Possible Cause: Carrier gas cylinder pressure too low to allow regulator to work properly                                                                                                                   
Replace the carrier gas cylinders.

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