Applied Analytical Systems


Noisy chromatograms, random spikes, and poor detector sensitivity are symptoms of a dirty FID — a common problem in gas chromatography. You will consistently obtain better chromatograms and reduce instrument downtime if you keep the FID clean.

The most common source of contamination in a flame ionization detector (FID) is bleed from silicone stationary phases and silylating reagents, which combust in the FID and produce silica. When deposited on surfaces within the detector, this white powder causes noisy chromatograms, random spikes, and poor detector sensitivity Figure below;

Figure 1. A Noisy Chromatogram, Caused by a Dirty FID

In this article we will

  1. methods of troubleshooting noise to confirm whether the source is a dirty FID,
  2. method of cleaning FIDs, and
  3. ways to reduce contamination in the future
    Before you shut down your instrument and clean your detector, it is wise to confirm that the problem is detector-related, rather than related to some other component of your system. The few, simple procedures described here can eliminate other possibilities as the source of the problem.
  • Carrier Gas and Stationary Phase

Seal the detector inlet in the oven with a  plug and ignite the detector. If the chromatogram noise disappears, then the source of the problem is contaminants in the carrier gas or bleed from the chromatography column, not a dirty FID.

  • Hydrogen and Air Systems

Hydrogen and air used in the sulfide can be a source of contamination, especially when problems emerged after replacing the cylinder. An incorrect flow rate in either source can cause noise, lack of sensitivity, and/or difficulty when igniting the flame. A contaminated cylinder of gas could be the source of the problem, especially if the noise appeared several hours after you changed a cylinder. Check each cylinder for contaminants and replace if necessary. To eliminate the problem of contaminated air, we recommend using a zero air generator

  • Electrical System

Electrical interference may exhibit similar symptoms dirty FID. There may be a defect electrometer, poor contact or interference by other devices in the lab. To isolate this source of noise, disconnect the electrometer cable(s) from the FID. If noise persists, it is coming from the electrical system.

Precautions before cleaning

  • Isolate electrical source, make sure to unplug the power cord!
  • Remember that the detector may be hot! be sure the collector assembly is cool before you begin
  • When dismantling FIDU pay attention insulating parts. Use tweezers, whether these parts do not transfer dirt from your hands or gloves. Beware of possible scratches.
  • Pay Attention ! Carefully note the distance from the collector assembly to the flame jet.

How to Clean an FID
To properly clean an FID, you must clean the
1. Collector assembly
2. The jets:
Jet cleaning  procedure.

  • Run a cleaning wire through the top of the jet. Run it back and forth a few times until it moves smoothly. Be careful not to scratch the jet. (Do not force too large a wire or probe into the jet opening or the opening will become distorted. A loss of sensitivity, poor peak shape and/or lighting difficulties may result if the opening is deformed.)
  • Fill an ultrasonic cleaning bath with aqueous detergent, and place the jet in the bath. Sonicate for five minutes.
  • Use a jet reamer to clean the inside of the jet.
  • Sonicate again for five minutes.
    NOTE: From this point on, handle the parts only with forceps!
  • Remove the jet from the bath and rinse it thoroughly, first with hot tap water and then with a small amount of GC-grade methanol.
  • Blow the jet dry with a burst of the compressed air or nitrogen, and then place the jet on a paper towel and allow it to air dry.
  1. The Teflon® or ceramic insulators: Ceramic parts of an FID are best cleaned with aqua regia, a 1:~3 mixture of concentrated nitric and hydrochloric acids, at ambient or mildly elevated temperature. Before treatment, remove all metal and rubber from the ceramic parts – aqua regia will attack these.
  2. The housing.

After you have cleaned all parts of the detector, check all Orings and replace them if necessary. Worn-out O-rings will cause gas leaks, which can produce detector noise or an increase in detector contamination. Reassemble the FID, light the flame, and allow the detector temperature to equilibrate at 10°C–50°C higher than the column will reach during typical operation. This will reduce the amount of phase condensing onto the detector parts. Do not exceed the maximum temperature limit of the stationary phase – many columns fit far enough into the detector to expose the phase to these elevated temperatures. Set the proper flow rates for hydrogen and compressed air (refer to the instrument manual), and ignite the flame. Turn on the electrometer and allow a few minutes for warmup. The flame should now be stable and noise-free.


  1. Conditioning:
    Most detector noise and contamination is the result of column bleed. The amount of bleed is greatest when the column is initially conditioned. Your detector will remain clean longer if you condition a new column before connecting it to the detector. Byproducts eluted during conditioning, potentially harmful to the FID, are voided into the oven. Connect the column inlet to the injector as usual. Place a restrictor at the column exit to prevent back diffusion of air into the column (exposure of a heated column to air can destroy the liquid phase). Purge the column with carrier gas at room temperature for a few hours before you begin the temperature program. Do not allow a combustible carrier gas such as hydrogen, methane, etc. to exit the column into the oven. Pipe these materials out of the oven and into a hood. (Be sure to attach a restrictor to the outlet of the pipeline in the hood.) Consult the column manufacturer for conditioning details, i.e., duration and temperature of conditioning. Do not routinely condition new columns at the maximum temperature limit of the stationary phase – this will reduce column life. Connecting a well-conditioned column to a clean FID should produce good sensitivity. If detector stability quickly degenerates, you should evaluate the quality of your stationary phase and carrier gas.
  2. Stationary Phase
    Use GC quality stationary phases whenever possible — they are purified to remove lower molecular weight components. Technical grade materials will bleed more than GC quality materials.
  3. Carrier Gas
    Moisture and oxygen in the carrier gas will cause stationary phase to deteriorate and bleed. Use chromatography-quality gases, and periodically monitor the gas system for leaks, which might allow atmospheric oxygen and water to enter the column.
  4. Septa
    Frequently check the septum for leaks. A leaking septum can allow oxygen and water to enter the carrier gas and cause the stationary phase to deteriorate and bleed. To check for leaks without contaminating the septum (and subsequent samples) with liquid leak detectors, use an electronic GOW-MAC leak detector, If you run your instrument frequently, we recommend you change the septum regularly.


Written by Oweh Gabriel,, [email protected]







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