GC troubleshooting

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Gamal A.Hamid
Contents

• Introduction

• Troubleshooting Categories:

1. Baseline

2. Peak Shapes And Sizes

3. Retention Time
4. Separation

5. Quantitation

6. Column Deterioration

7. Ghost Peak

8. Broad Solvent Front

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Gamal A.Hamid
 Simple checks

In order to reduce the troubleshooting follow the simple checks:

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Troubleshootin
1. Gases - pressures, carrier gas average linear velocity,
and flow rates (detector, split vent, septum purge).
2. Temperatures - column, injector, detector .
3. System parameters - purge activation times, detector attenuation, mass
ranges, etc.
4. Gas lines and traps - cleanliness, leaks, expiration.
5. Injector consumables - septa, liners, O-rings and ferrules.
6. Sample integrity - concentration, degradation, solvent, storage.
7. Syringes - handling technique, leaks, needle sharpness, cleanliness.
8. Data system - settings and connections.

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Gamal A.Hamid
 Troubleshooting categories

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1. Baseline disturbances.
2. Irregular peak shapes or sizes.
3. Retention time shifts.
4. Loss of separation or resolution.
5. Quantitation difficulties.
6. Rapid column deteriorations.
7. Ghost peaks .
8. Broad solvent fronts.

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Gamal A.Hamid
 Troubleshooting Tools

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1. An electronic leak detector
2. A flow meter
3. An accurate thermometer
4. A reliable analytical column
5. New syringes
6. Spare septa and high temperature septa
7. Spare ferrules
8. Detector cleaning solutions
9. Spare recorder and electrometer cables
10. Instrument manuals

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Gamal A.Hamid
Baseline troubleshooting

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Gamal A.Hamid
 Rising Baseline
Chromatogram Reason
1. There is bleeding from the
GC column.
2. Air is leaking into the
system.
3. Injector contaminated.
4. Column contaminated.
5. Detector contaminated.
6. Increase of temperature
too fast.
7. Poor gas quality.
Solution
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Troubleshootin
1. Condition or change the
column.
2. Trace and repair the leak.
3. Make a run at lower injector
temperature; if the baseline
improves, replace liner, use low
bleed or high temperature
septa.
4. Cut two turns from column
entrance; rinse column with
solvent (only chemically bonded
phases); otherwise replace
column or use guard column.
5. Clean detector.
6. Decrease temperature gradient
and end temperature.
7. Use gas grades recommended
for gc.
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Gamal A.Hamid
 Declining Baseline

Chromatogram Reason Solution

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Troubleshootin
1. Gas flow changes with 1. Check gas content in gas
temperature gradient. cylinder; pressure must be a few
2. Contaminated gas/ poor bar above the required pressure
gas quality (at constant at max. Temperature; otherwise
inlet pressure). exchange gas cylinder.
3. Column not properly 2. Check gas supply.
installed. 3. Check column installation (fid).

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Gamal A.Hamid
 Regular Spikes
Chromatogram Reason
1. FID: condensate or dust
particles in detector.
2. Contaminated carrier,
makeup, or other gas.
3. Defective electronics or
detector.
Solution
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1. Clean detector and check ends
of column for particles. If
particles are present, rinse
column (bonded phase only) or
remove 1-2 coils from
contaminated end .
2. Use only high quality gases;
install high performance gas
purifiers.
3. Troubleshoot electronics and
detector according to steps.
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Gamal A.Hamid
 Irregular Spikes
Chromatogram Reason
1. Defective detector cable
(intermittent short-
circuiting).
2. ECD: heater wires and
detector wires loose or too
close together.
3. FID: insufficient hydrogen
flow.
4. Electronic interference
from external source.
Solution
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1. Troubleshoot according to steps
described on page 2. Replace
cable if necessary.
2. Check wire connections and
positions, relocate if necessary.
3. Monitor hydrogen flow, increase
if necessary.
4. Relocate instrument, identify
interference source (e.g.,
nearby transmitter site, etc.)
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Gamal A.Hamid
 Baseline Drift Downward “ falling”

Chromatogram Reason Solution

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1. Carrier gas leak in the 1. Perform a leak test and check
system. the tightness of the connections
2. Column is baking out. on the carrier gas line.
2. Allow enough time for the
column to stabilize.

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Gamal A.Hamid
 Baseline Drift Upward “Rising”

Chromatogram Reason Solution

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1. Accumulation of stationary 1. Remove the end section of the
phase. column.
2. Carrier gas cylinder 2. Replace the carrier gas cylinder,
pressure too low to allow or increase the pressure.
control. 3. Check the gas controllers.
3. Drifting carrier gas or 4. Check impurity levels in the gas
combustion gas flows. source. Use correct gas purity.
4. Accumulation of impurities
in the column.

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Gamal A.Hamid
 Irregular Baseline “Unstable”

Chromatogram Reason Solution

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1. Detector contaminated. 1. Bake out or clean the detector.
2. Excessive column bleed 2. Reduce the upper column
during column temperature. Bake out the
Temperature programming. column. Install a high
3. Oxygen contamination is temperature column.
decomposing the 3. Install oxygen filters in the carrier
stationary phase. gas line. Check the pneumatic
and inlet systems for leaks. Use
correct gas purity with low
oxygen content.

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Gamal A.Hamid
 Strong Noise

Chromatogram Reason Solution

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1. Leak at column entrance 1. Search for leaks; replace
ferrules.
or injection septum. 2. Make a run with lower injector
2. Bleeding of septum / temperature; if the baseline
improves, replace liner,
3. injector contaminated. 3. Use low bleed or high
4. Column contaminated. temperature septa.
4. Cut two turns from column
5. Column not properly entrance; rinse column with
conditioned. solvent (only chemically bonded
phases); otherwise replace
6. Detector contaminated column or use guard column.
(electronics). 5. Condition column (while column
is not connected to the
7. Increase of temperature detector).
too fast. 6. Clean detector
7. Decrease temperature gradient.
8. Poor gas quality. 8. Use gas grades recommended
for GC.

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Gamal A.Hamid
 Plateaus

Chromatogram Reason Solution

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1. Steps in temperature 1. Avoid very short and strong
program too drastic. heating periods.

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Gamal A.Hamid
Peak troubleshooting

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Gamal A.Hamid
 No Peaks after solvent peak

Chromatogram Reason Solution

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1. Carrier gas flow too high. 1. Reduce the carrier gas flow.
2. Combustion gas flow 2. Check the combustion gas flow.
incorrect. 3. Bake out or clean the detector.
3. Detector contaminated 4. Check the detector
4. FID flame 5. Inject less sample.
5. Too much sample injected. 6. Check the column position.
6. Incorrect column position
in S/SL injector (too high).

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Gamal A.Hamid
 No Peaks at all
Chromatogram Reason
1. Syringe or autosampler
blocked.
2. Injector temp. very low.
3. Column temperature very
low.
4. Column broken.
5. No flow of carrier.
6. Detector off.
7. Data recording problem.
8. Incorrect column position
in S/SL injector (too high).
Solution
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1. Check the syringe.
2. Increase temp about 50°C
higher than the boiling point of
the least volatile component
of the sample.
3. Increase the oven temp.
4. Replace the column.
5. Measure and check the carrier
flow.
6. Turn on.
7. check recording problem.
8. Check the column position.
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Gamal A.Hamid
 Small Peaks
Chromatogram Reason
1. Concentration not
compatible with the
dynamic range of the
detection system.
2. Inappropriate injection
technique.
3. Injection parameters
inappropriate.
4. Leaking syringe or septum.
5. Leaks at the injection.
6. Poor injection technique.
7. Poor split flow or ratio
control.
Solution
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Troubleshootin
1. Ensure that the sample
concentration is suitable for the
detection system.
2. Try a different injection
technique.
3. Check the injection temperature
and flow rates.
4. Check and replace the syringe
and/or septum at regular
intervals.
5. Check the column connections.
Run a leak check.
6. Carefully meter the injected
amount. Use a clean, good-
quality syringe.
7. Monitor the flow. Replace the
in-line filter.
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Gamal A.Hamid
 Missing Peak

Chromatogram Reason Solution

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Troubleshootin
1. Syringe defective / 1. Use a different syringe or clean it.
clogged. 2. Increase injection volume; conc.
2. Sample too diluted. Sample.
3. Sample concentration 3. Decrease volume; dilute sample.
too high. 4. Check column installation; search for
4. Column connection leaks; replace ferrules. Replace
leaks, column not septum.
properly installed 5. Increase injector temperature.
6. Check temperature program; reduce
perforated injection injector temperature; replace liner;
septum. check capillary ends.
5. Injector temperature 7. Check temperature program, oven
too low. temperature (external thermometer);
6. Sample decomposes in decrease temp.
the injector. 8. Measure flow, control and adjust it if
7. Column oven too hot. necessary.
8. Incorrect flow rate. 9. Check capillary ends; check intact
9. Column absorbs or deactivation using the test mixture; for
decomposes analyte. poor results shorten both column ends
by about 10 cm; or replace column;

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Gamal A.Hamid
 Interfering Peaks
Chromatogram Reason
1. Poor gas quality.
2. FID: dust or contaminants
in the detector.
3. Electronic defect,
damaged cable or
detector.
4. Bleeding of silicon septa.
Solution
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Troubleshootin
1. Use gas grades recommended
for GC.
2. Clean detector; if particles are
visible in the column or column
ends are not cut precisely
(frayed edges), cut two turns
from the column entrance.
3. Replace cable.
4. Replace injection septum, use
low bleed or high temperature
septa.
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Gamal A.Hamid
 Broad peaks
Chromatogram Reason
1. Column flow too high.
2. Column flow too low.
3. Split flow too low in split
injection.
4. Column performances
degraded.
5. Dirty injector.
6. Stationary phase
accumulated in the outlet.
7. Detector base body
temperature too low.
8. The sample is overloading
the column.
Solution
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1. Reduce the flow to slightly
above optimum.
2. Increase the flow to slightly
above optimum.
3. Increase the flow to 40-50
ml/min.
4. Test the column at the optimum
flow rate.
5. Clean or replace the liner.
6. Remove the last two coils from
the column.
7. Increase the temperature to 5°C
below the column maximum.
8. Reduce the amount and/or
concentration of the sample.
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Gamal A.Hamid
 Double Peaks

Chromatogram Reason Solution

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1. Injection speed too low 1. Inject more rapidly in a smooth
2. Wrong autosampler motion.
injection speed or mode. 2. Use a higher speed.

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Gamal A.Hamid
 Negative Peak

Chromatogram Reason Solution

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1. All Peaks negative 1. Correct the connections.
Integrator wires reversed.
2. Some Peaks negative 2. None required
This symptom can be
normal.

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Gamal A.Hamid
 Front Tailing “fronting”
Chromatogram Reason
1. Column or detector
overloaded.
2. Column temperature too
low.
3. Stationary phase too thin.
4. Poor injection technique.
Solution
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Troubleshootin
1. Decrease the injected amount
and/or analyte concentrations.
Increase the split ratio.
2. Increase the temperature.
3. Use a thicker-film column.
4. Repeat, with better injection
technique
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Gamal A.Hamid
 Sample Tailing
Chromatogram Reason
1. Column degradation
causing activity.
2. Column/oven temperature
too low.
3. Dirty liner.
4. Glass wool or inlet liner
causing activity.
5. Inlet temperature too low
Poor or obstructed column
connections.
6. Wrong stationary phase.
Solution
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Troubleshootin
1. Inject a test mixture and
evaluate the column.
2. Increase the column/oven
temperature.
3. Clean or replace the liner.
4. Replace with fresh salinized
wool and a clean inlet liner.
5. Increase the inlet temperature.
Remake the column inlet
connection.
6. Replace the column.
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Gamal A.Hamid
 Solvent Tailing

Chromatogram Reason Solution

1. Incorrect column position
in inlet.
2. Initial oven temperature
too high (On Column).
3. Septum purge flow too low
and/or split/splitless vent
flow too low.
4. Too large injection size.
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1. Reinstall the column
2. Reduce the initial oven
temperature.
3. Check and adjust the septum
purge and vent flows.
4. Reduce the injection size.

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Gamal A.Hamid
 Cut Tops “Clipping”

Chromatogram Reason Solution

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1. Data system zoomed in too 1. Zoom out to view the entire
close. chromatogram.
2. Detector or integrator 2. Set the attenuation higher.
attenuation set too low.
3. Detector range too 3. Set a less-sensitive detector
sensitive. range.
4. Incorrect input to recording 4. Correct and check the recording
unit. unit

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Gamal A.Hamid
 Leading Peak

Chromatogram Reason Solution

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Troubleshootin
1. Column overloaded. 1. Decrease sample size.
2. Increase sensitivity and reduce
2. Two compounds eluting sample size. Reduce column
simultaneously. temperature approximately
20°C and look for partial
3. Sample condensing in separation.
injector or column. 3. increase temperature(s) as
necessary .
4. Sample decomposing. 4. Verify injector, detector, and
oven temperatures with an
accurate thermometer, adjust if
necessary. If instrument settings
and thermometer agree, reduce
temperature(s). If column
performance is not restored,
replace column. Remove inlet
liner and check cleanliness. Use
new, deactivated liner or
replace glass wool and packing.

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Gamal A.Hamid
 Peaks on the hill
Chromatogram Reason
1. Column not properly
installed.
2. Temperature of injection
too low.
3. Solvent not compatible
with gc phase.
4. Splitter defect.
5. Poorly deactivated column,
film thickness too low.
Solution
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Troubleshootin
1. Check capillary ends; check tight
and correct fit in injector and
detector.
2. Check injector temperature; if
analytes are stable, increase
temperature.
3. Change solvent.
4. Measure flow and adjust
splitter.
5. Check capillary ends; check
intact deactivation using the
test mixture; for poor results
shorten both column ends by
about 10 cm; or replace column.
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Gamal A.Hamid
Resolution troubleshooting

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Gamal A.Hamid
 Loss of Resolution

Chromatogram Reason Solution

1. Carrier gas flow rate too
high.
2. Column deteriorated.
3. Column temperature too
high.
4. Column too short.
5. Incorrect column choice.
6. Injection technique is not
adequate.
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Troubleshootin
1. Reduce the carrier gas flow rate.
2. Replace the column.
3. Lower the column oven
temperature.
4. Use a longer column.
5. Install a suitable column.
6. Choose a correct injection
technique.

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Gamal A.Hamid
 Poor Responding “Sensitivity”

Chromatogram Reason Solution

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1. Leaks in the GC carrier gas 1. Run a leak test and correct
line. leaks.
2. Syringe leaks during 2. Replace syringe or piston seals,
injection. if applicable.
3. Split injection temperature 3. Increase the temperature of the
too low. injector.
4. Column is in poor 4. Condition or change the column
condition, or wrong column
type used.

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Gamal A.Hamid
Retention troubleshooting

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Gamal A.Hamid
 Increasing Retention” Prolonged”

Chromatogram Reason Solution

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1. Increasing carrier leakage. 1. Check the septum and column
connections.
2. Carrier gas supply running 2. Replace the bottle.
out.

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Gamal A.Hamid
 Decreasing Retention “ Shortened”

Chromatogram Reason Solution

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1. Stationary phase 1. Use a carrier gas free of oxygen
deteriorated by oxygen and water.
and/or water. 2. Reduce the column
2. Stationary phase loss due temperature.
to column bleeding.

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Gamal A.Hamid
 Drafting Retention
Chromatogram Reason
1. Drifting or unstable
pneumatic controller
2. Poor injection technique
3. Sample size is too large
4. Unstable column
temperature
Solution
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Troubleshootin
1. Monitor the column pressure or
flow. Check and replace the
controller if necessary.
2. Start the run at consistent time
after injection
3. Reduce the injected amount.
4. Check the main oven door and
cooling flap. Monitor the
column temperature
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Gamal A.Hamid
 Inconsistent Retention

Chromatogram Reason Solution

1. GC column is in poor
Condition
2. Insufficient equilibrium
time set on GC.
3. Poor injection
4. Fast heating ramp
5. Air leak in the system in
injector seal or the carrier
gas manifold.
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Troubleshootin
1. Condition or change the column
2. Increase equilibrium time
3. Repeat with suitable injection
technique
4. Reduce heating ramp.
5. Trace and repair air leakage

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Gamal A.Hamid
Others troubleshooting

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Gamal A.Hamid
 Bleeding
Chromatogram Reason
1. Decomposition of the
stationary phase.
2. Column contaminated.
3. Increase of temperature
too fast / end temperature
too high.
4. Column not properly
conditioned.
5. Detector contaminated.
6. Poor gas quality.
Solution
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Troubleshootin
1. Check for leaks; matrix check
for compatibility with the column
2. Cut two turns from column
entrance; rinse column with
solvent (only chemically bonded
phases); otherwise replace
column or use guard column.
3. Decrease temperature gradient
and end temperature.
4. Condition column according to
manufacturers’ instructions
(while column is not connected
to the detector).
5. Clean detector
6. Use gas grades recommended
for gc; for longer supply lines
from gas source to gc use gas
purification cartridges directly
connected to the gc.
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Gamal A.Hamid
 Ghosts Peaks
Chromatogram Reason
1. Contaminated carrier gas.
Contamination from
laboratory glassware.
2. Decomposition of injected
sample.
3. Dirty injection solution.
Solution
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Troubleshootin
1. Replace the cylinder or replace
the filter.
2. Ensure the glassware is clean
and contamination-free.
3. Decrease the injection port
temperature. Use the on-
column injection technique.
Carry out adequate clean-up of
sample prior to injection.
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Gamal A.Hamid
 Broad Solvent Peak
Chromatogram Reason
1. Column installed poorly,
producing dead volume in
injection port.
2. Normal condition with very
dilute sample, as in trace
analysis.
3. Poor injection technique.
4. Injection port temperature
too low.
5. Sample solvent interacting
with detector.
6. Sample solvent retained by
column (e.g., methanol by
active column).
7. Septum purge plugged or
turned off.
8. Incorrect split flow in split
injection mode.
Solution
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Troubleshootin
1. Check column connections and
correct if necessary.
2. Use on-column injection.
3. Ignore.
4. Review injection technique
Verify temperature with an
accurate thermometer, adjust if
necessary. If instrument setting
and thermometer agree,
increase temperature (do not
exceed stationary phase limit)
or inject sample directly onto
column.
5. Change solvent.
6. Change solvent.
7. Check purge, adjust if necessary.
8. Measure split flow, adjust if
necessary.
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Gamal A.Hamid