Header Ads Widget

GC Troubleshooting Tips

Many GC problems can be prevented if the column is properly installed and GC is maintained routinely. For example, replacing septa or liner at regular intervals and keeping the injector and detector clean and well-maintained should solve many problems. Regular preventive maintenance depends on a particular model of GC and you should consult required operations in the operator's and service manuals.

  • Follow these basic troubleshooting steps to isolate problems related to the sample, injector, detector, and column.
  • Check the obvious explanations first and change only one thing at a time until you identify and resolve the problem.

Check the Obvious
  1. Power supply
  2. Electrical connections
  3. Signal connections
  4. Gas purity
  5. Gas flows
  6. Temperature settings
  7. Syringe condition
  8. Sample preparation
  9. Analytical conditions

Identify the Cause
  • Define the problem clearly; for example, “Over the last 4 days, only the phenols in my sample have been tailing.”
  • Review sample and maintenance records to identify trends in the data or problem indicators, such as area counts decreasing over time or injector maintenance not being performed as scheduled.
  • Use a logical sequence of steps to isolate possible causes.

Document Work and Verify System Performance
  • Document all troubleshooting steps and results; this may help you identify and solve the next problem faster.
  • Always inject a test mix and compare it to previous data to ensure restored performance.

  • An analyst observed that no peaks appeared during a GC-FID analysis. The flowchart below shows a logical progression of steps that can be used to identify the cause and correct the problem.

Good chromatography is critical to obtaining accurate, reproducible results.  Co-elutions, asymmetric peaks, baseline noise, and other issues are common challenges in the GC laboratory. These analytical problems and others can be overcome by troubleshooting your separations using the tips below.

Poor Resolution



Non-selective stationary phase

Choose appropriate stationary phase and column dimensions.

Poor efficiency

Optimize carrier gas linear velocity and GC oven temperature program.

Sample overload

Adjust sample concentration or amount on a column.

Incorrect analytical conditions used

Verify temperature program, flow rates, and column parameters.

Poor Retention Time Reproducibility




Leak check injector and press-t connections.

Replace critical seals (i.e., septa, O-rings, inlet disc, etc.)

Analyte adsorption

Maintain inlet liner and GC column.

Use properly deactivated liners, seals, and columns.

Resolution/integration issues

Avoid sample overload.

Incorrect column/oven temperature program

Verify column temperature and oven temperature program.

Incorrect or variable carrier gas ­ow rate/linear velocity

Verify the carrier gas ­ow and linear velocity. Repair or replace parts if necessary.

Poor control of oven temperature programming

Confirm GC oven program falls within the instrument manufacturer’s recommendation.

Incorrect oven equilibration time

Extend GC oven equilibration time.

If manual injection, delay between pushing start and actual injection

Use autosampler or standardize manual injection procedure.

Fronting Peaks
Fronting peaks are usually the result of column overloading. In this case, the effect should be a function of injection volume. Solutions include reducing the injection volume or using a column with greater capacity. Columns with larger diameter or thicker stationary phase coatings generally have larger sample capacities, however, resolution may be reduced.



Incompatible stationary phase

Choose appropriate stationary phase.

Column overloading

Reduce amount injected, dilute sample.

Increase column inner diameter and/or fi­lm thickness.

PEOPLE ALSO READ: General HPLC Column Care

Tailing Peaks



Adsorption due to surface activity or contamination

Use properly cleaned and deactivated liner, seal, and column.

Trim inlet end of the column.

Replace column if damaged.

Adsorption due to the chemical composition of a compound

Derivatize compound.

Leak in system

Check for leaks at all connections, and replace critical seals if needed.

Installation issues

Minimize dead volume.

Verify that the column is cut properly (square).

Verify correct installation distances.

Contaminated or active injector liner, seal or column

Clean or replace injector liner. Do not use glass wool in the liner. If necessary, replace the column.

Dead volume due to poorly installed liner or column.

Confirm by injecting inert peak (methane). If it tails, the column is not properly installed. Reinstall liner and column as necessary.

Ragged column end

Score the tubing lightly with a ceramic scoring wafer or sapphire scriber before breaking it. Examine the end using a magnifying glass. If the break is not clean and the end square, cut the column again. Point the end down while breaking it and while installing a nut and ferrule to prevent fragments from entering the column.

Reinstall the column.

A bad match between the polarities of the stationary phase and the solvent

Change the stationary phase. Usually, polar analytes tail on no polar columns or dirty columns.

A cold region in the sample flow path

Remove any cold zones in the flow path

Debris in the liner or column

Clean or replace the liner. Cut 10 cm off the end of the column and reinstall it.

Injection takes too long.

Improve injection technique.

Split ration is too low

Increase split ratio to at least 20:1

Overloading the inlet

Decrease the sample volume or dilute sample

Some types of compounds such as alcoholic amines, primary and secondary amines and carboxylic acids tend to tail.

Try a more polar column. Make a derivative of the sample.

Split Peaks



Mismatched solvent/stationary phase polarity

Adjust solvent or stationary phase to allow wetting.

Incomplete vaporization

Add surface area, such as wool, to the inlet liner to enhance vaporization.

Use proper injector temperature.

Sample loading capacity exceeded

Inject less sample (dilute, use split injection, reduce injection volume).

Fast autosampler injection into open liner

Use wool or slow injection speed.

Fluctuations in column temperature

Repair temperature control system

Mixed sample solvent for splitless or on-column injections

Use single solvent

When using injection techniques that require "solvent effect" refocusing such as splitless injection, the solvent must form a compact, continuous flooded zone in the column. If the solvent does not wet the stationary phase sufficiently as might be the case for methanol used with a nonpolar stationary phase, the solvent flooded zone may be several meters long and not of uniform thickness. This will result in broad and distorted peaks because the solutes will not be refocused into a narrow band near the beginning of the column.

Installing a retention gap (5 meters of uncoated but deactivated column) ahead of the chromatographic column may reduce or eliminate this problem.

Carryover/Ghost Peaks



Contaminated syringe or rinse solvent

Replace rinse solvent.

Rinse or replace syringe.

Backflash (sample volume exceeds liner volume)

Inject a smaller amount.

Use a liner with a large internal diameter.

Increase head pressure (i.e., flowrate) to contain the vapor cloud.

Use slower injection rate.

Lower inlet temperature.

Increase split flow.

Use liner with packing.

Use pressure-pulse injection.

Last analysis ended too soon

Extend analysis time to allow all components and/or matrix interferences to elute.

Remmants of previous samples in the inlet or column. Ghost peaks due to remmants are most likely to occur when increasing inlet or column temperatures.

Increase the final temperature and lengthen the run time to allow for complete elution of previous samples. If ghost peaks continue to occur, clean the inlet. Condition the column at temperature higher than has been used but lower than the maximum continuous operation temperature for the column. Cut 10 cm off the inlet end of the column and/or reverse it before reconditioning it. If it does not help, replace the column.

Backflash may cause remmants.

Backflash refers to vapors from the sample which expand to exceed the volume of the injector liner. These vapors may come in contact with colder spots, such as the septum and gas inlets of the injector. Less volatile components may condense. These condensates may

vaporize later and interfere with subsequent analyses, sometimes producing "ghost peaks".

Use septum purge

Lower injection volume

Enlarge injector liner

Optimize injector temperature

Use pressure pulsed program

High Bleed



Improper column conditioning

Increase conditioning time and/or temperature.


Trim column and/or heat to maximum temperature to remove contaminants.

Replace carrier gas and/or detector gas filters.

Clean injector and detector.

Leak in system and oxidation of stationary phase

Check for oxygen leaks across the entire system and replace seals and/or filters.

Replace column.

Baseline Problems

Baseline problems could be divided into 5 categories.
  1. Drift means slow baseline movement in one direction.
  2. Noise is rapid and random movement of the baseline position
  3. Offset is sudden unexplained change of the baseline position
  4. Spiking is presented by peaks with no width, either positive or negative
  5. Wander is low frequency noise



Carrier gas leak or contamination

Leak check connections and replace seals if needed.

Replace carrier gas and/or detector gas filters.

Injector or detector contamination

Clean system and perform regular maintenance.

Column contamination or stationary phase bleed

Condition, trim, and rinse column.

Septum coring/bleed

Replace septum.

Inspect inlet liner for septa particles and replace liner if needed.

Loose cable or circuit board connections

Clean and repair electrical connections.

Variable carrier gas or detector gas flows

Verify flow rates are steady and reproducible; may need to replace or repair flow controller.

Leak check system.

Detector not ready

Allow enough time for detector temperatures and flows to equilibrate.


Electrical disturbances entering the chromatograph through power cables, even shielded cables

Try to correlate spikes with events in equipment near the chromatograph. Periodicity is often a clue. Turn off equipment or move it. If necessary, install a voltage regulator.


The column may be inserted too far into the flame of an FID, NPD or FPD detector

Reinstall the column. Be sure to insert the column into the detector exactly the correct distance specified in the instrument manual.

An air leak can result in noise in ECD and TCD detectors

Eliminate the leak.

Incorrect combustion gases or flow rates can generate noise in FID, NPD or FPD detectors.

Be sure your gases are the proper grade, as well as clean and dry. Reset the flow rates of the gases to their proper values.

Contaminated injector

Clean injector. Replace inlet liner, septa and seals.

Contaminated column

Bake out the column. Cut off first 10 cm of column. If it does not help, replace the column.

Defective detector

Clean and/or replace parts as necessary.

Defective detector board

Consult GC manufacturer.

Downward drift

Downward drift for a few minutes is normal after installing a new column

Increase the oven temperature to close to the maximum continuous operating temperature for the column. Maintain the temperature until flat baseline is observed. If the detector signal does not drop in 10 minutes, immediately cool the column and check for leaks.

Unequilibrated detector

Allow sufficient time for temperature equilibration of the detector.

Downward drift is frequently due to the "back-out" of contaminants from the detector or other parts of the GC

Clean out contamination.

Upward drift

Damage to the stationary phase of the GC column

Determine the cause of the damage. It may be due to impurities in the carrier gas or to excessive temperatures. Replace column.

Drift in gas flow rates

Clean or replace flow or pressure regulator(s). Adjust pressure.


Line voltage changes

Monitor line voltage for correlation with offset. If correlation is found, install voltage regulator or ensure stable power supply.

Poor electrical changes

Check electrical connections. Tighten any loose connections. Clean any dirty or corroded connections.

Contaminated injector

Clean injector. Replace inlet liner, septa and seals.

Contaminated column

Bake out the column. Cut off first 10 cm of column. If it does not help, replace the column.

Column inserted too fat into the flame of FID, NPD or FPD detectors

Reinstall the column. Be sure to insert the column into the detector exactly the correct distance specified in the instrument manual.

Contaminated detector

Clean the detector if possible.


Baseline wandering may be caused by changes in environmental conditions such as temperature or line voltage

Try to correlate the wandering with environmental parameters. If a correlation is observed, you will know what to do.

Inadequate temperature control Check if variations can be correlated with changes in the baseline position.

Measure detector temperature.

Wandering while using isothermal conditions may be due to contaminated carrier gas

Change the carrier gas or the gas purification traps.

Contaminated injector

Clean injector. Replace inlet liner, glass wool and seals.

Contaminated column

Bake out the column. Cut off first 10 cm of column. If it does not help, replace the column.

Response Variation



Sample issues

Check sample concentration.

Check sample preparation procedure.

Check sample decomposition/shelf life.

Syringe problems

Replace syringe.

Check autosampler operation.


Verify signal settings and adjust if needed.

Repair or replace cables or boards.

Dirty or damaged detector

Perform detector maintenance or replace parts.

Flow/temperature settings wrong or variable

Verify steady ow rates and temperatures, then adjust settings and/or replace parts if needed.


Remove contamination and use properly deactivated liner, seal, and column.


Check for leaks at all connections and repair connections as needed.

Change in sample introduction/injection method

Verify injection technique and change back to original technique.

Check that split ratio is correct.

Verify that the splitless hold time is correct.

No Peaks



Injection problems

Plugged syringe; clean or replace syringe.

Verify there is sample in the syringe.

Injecting into wrong inlet; reset autosampler.

Verify carrier gas is flowing.

Broken column

Replace column.

Column installed into wrong injector or detector

Re-install column.

Detector problems

Signal not recorded; check detector cables and verify that detector is turned on.

Detector gas turned off or wrong flow rates used; turn detector on and/or adjust flow rates.

Defective syringe

Try a new or proven syringe.

"Blown" septum or massive leaks at the inlet

Find and fix leaks.

Problems with carrier gas flow

Adjust gas flow. Check the column flow path the column outlet by immersion to methanol.

Broken column or column installed in the wrong way

Replace or reinstall the column.

The detector is not functioning or not connected to the recorder or integrator.

Ensure that detector is working properly. E.g.: Is the flame in a FID on? Check connection to the output device.

Broad Peaks



High dead volume

Minimize dead volume in the GC system; verify proper column installation, proper connectors, proper liners, etc.

Low flow rates

Verify injector and detector flow rates and adjust if needed. Verify make-up gas flow and adjust if needed.

Slow GC oven program

Increase GC oven programming rate.

Poor analyte/solvent focusing

Lower GC oven start temperature.

Column film is too thick

Reduce retention of compounds by decreasing film thickness and length.

Sample carryover

See Carryover/Ghost Peaks solutions.

Distorted Peak Shapes



All peaks reduced in size

Sample validity

Check the concentration and stability of the sample.

Flattened top peaks

Detector overload. The broad peaks may have a rounded top or even valleys at the top.

Reduce sample volume, dilute with solvent, or use a higher split ratio.

Overload of the signal processing electronics. The peaks are clipped with flat tops.

Attenuate detector output or reduce sample amount.

Irreproducible peak heights or areas

Inconsistent injection

Develop a reproducible injection technique. Use autosampler.

Distorted peak shapes can adversely affect quantitative determinations

Correct any problems that result in the distortion of peak shape. See Peak shape problems.

Baseline disturbances

See Baseline problems.

Variations in GC operating parameters

Standardize operating parameters.

Negative peaks

The incorrect polarity of the recorder

Reverse polarity of recorder connections.

Incorrect set up in the software

Set up the right parameters in your chromatography software.

The sample compound has greater thermal conductivity than the carrier gas and you are using a TCD or µTCD detector

If possible, change carrier gas. Otherwise, there is not a solution.

Detector overload in element-specific detectors such as ECD, NPD, FPD, etc., can produce both positive and negative peaks

Have the compound of interest arrive at the detector at a different time from the solvent or other compounds in high concentration. H produces negative peaks with TCD (μTCD) and helium carrier gas.

A dirty ECD detector can give a negative peak after a positive one

Clean or replace the ECD detector.

Selective Sensitivity Loss



Contamination of column and/or liner can lead to loss of sensitivity for active compounds

Clean liner. Bake out the column or replace it.

Injector leaks reduce the peak height of the most volatile components of a sample more than less volatile

Find and fix any leaks.

Initial column temperature is too high for splitless injection which can prevent refocusing of a sample. This affects the more volatile components most.

The initial column temperature should be below the boiling point of the solvent. Decrease the initial column temperature or use a less volatile solvent.

Inlet discrimination. The injector temperature is too low. Later eluting and less volatile compounds have a low response.

Increase injection temperature.

Retention Time Shifts



Change in column temperature

Check GC oven temperature

Change in gas flow rate (linear velocity)

Inject a detectable unretained sample such as methane to determine the linear gas velocity. Adjust gas pressure or flow to obtain proper values for your analytical method.

Leak in the injector

Check the septum first. Change, if necessary. Find the leak and fix it.

Change of solvent

Use the same solvent for standards and samples.

Contaminated column

Bake out the column. Cut 10 cm off the end of the column. If necessary, replace the column.

Loss of Resolution



Damage to stationary phase of column

Replace the column. This is usually indicated by excessive column bleeding or peak tailing.

Injector problems

Check for leaks, inappropriate temperature, split ration, purge time, dirty liner, glass wool in liner.

Large increase in sample concentration

Dilute sample

Inject less

Use higher split ratio

Broad Solvent Front



Bad column installation

Reinstall column

Injector leak

Find and fix leak

Injection volume too large

Decrease sample size or dilute it

Injection temperature too low

Increase injection temperature so the entire sample is vaporized "instantly". An injection temperature higher than the temperature limit of the column will not damage the column.

Split ratio is too low

Increase split ratio.

Column temperature too low

Increase column temperature (be careful on maximum column temperature limit). Use a lower boiling solvent.

Initial column temperature too

high for splitless injection

Decrease the initial column temperature. Use a less volatile solvent so the initial column temperature is below the solvent boiling point.

Purge time too long (splitless injection)

Use a shorter purge valve close time.

Rapid Column Performance Degradation



Broken column

Replace column. Avoid damaging the polyimide coating on the column. Avoid temperatures above the maximum column temperature limit. Avoid abrasion of the column. Remember, even if the column does not break immediately when the protective coating is damaged the column may possibly break spontaneously later.

Column too hot for too long

Replace the column. Stay below the limits specified for the column.

Exposure to oxygen, particularly at elevated temperatures

Find and fix any leaks. Be sure carrier gas is sufficiently pure.

Chemical damage due to inorganic acids or bases

Keep inorganic acids or bases out of the column. Neutralize samples.

Contamination of the column with nonvolatile materials

Prevent nonvolatile materials from getting into a column. For example, use a guard column.

Post a Comment