- 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.
- Power supply
- Electrical connections
- Signal connections
- Gas purity
- Gas flows
- Temperature settings
- Syringe condition
- Sample preparation
- Analytical conditions
- 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 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.

Causes |
Solutions |
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. |
Causes |
Solutions |
Leaks |
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. |
Causes |
Solutions |
Incompatible stationary
phase |
Choose appropriate stationary
phase. |
Column overloading |
Reduce amount injected, dilute
sample. Increase column inner diameter
and/or film thickness. |
Causes |
Solutions |
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
Causes |
Solutions |
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
Causes |
Solutions |
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 |
Causes |
Solutions |
Improper column
conditioning |
Increase conditioning time and/or
temperature. |
Contamination |
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. |
- Drift means slow baseline movement in one direction.
- Noise is rapid and random movement of the baseline position
- Offset is sudden unexplained change of the baseline position
- Spiking is presented by peaks with no width, either positive or negative
- Wander is low frequency noise
Causes |
Solutions |
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. |
Spiking |
|
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. |
Noise |
|
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. |
Offset |
|
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. |
Wander |
|
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. |
Causes |
Solutions |
Sample issues |
Check sample concentration. Check sample preparation
procedure. Check sample decomposition/shelf
life. |
Syringe problems |
Replace syringe. Check autosampler operation. |
Electronics |
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. |
Adsorption/reactivity |
Remove contamination and use
properly deactivated liner, seal, and column. |
Leaks |
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. |
Causes |
Solutions |
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. |
Causes |
Solutions |
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. |
Causes |
Solutions |
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. |
Causes |
Solutions |
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. |
Causes |
Solutions |
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. |
Causes |
Solutions |
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 |
Causes |
Solutions |
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. |
Causes |
Solutions |
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. |
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