GC Troubleshooting Guide

Your guide to solving common problems and staying productive

Checking the Basics Condensation Test Ghost Peaks Possible Cause

Contaminants introduced
Solution
Sample or solvent cleanup
Comments
Contaminants in sample process
Split Peaks Possible Cause
Injection technique
Solution
Change technique
Comments
Usually related to erratic plunger
or Carryover with sample or solvent depression or having sample in
A surprising number of problems involve fairly simple Use this test whenever injector or carrier gas Inlet contamination Clean the injector, replace liner,
gold seal, and septum
Try a condensation test;
gas lines may also need cleaning.
the syringe needle. Use an auto
injector

and often overlooked components of the GC system contamination problems are suspected (e.g., ghost Clean Blank Run (no injection) Take steps to prevent sample
backflush (reduce injection volume,
Mixed sample solvent Change sample solvent to
a single solvent
Worse for solvents with large
differences in polarity or boiling
or analysis. Many of these items are transparent in peaks or erratic baseline). lower inlet temperature, use larger
volume liner)
points

the daily operation of the GC and are often taken for

Poor column installation Reinstall the column Usually a large error in the insertion
Septum bleed Replace septum Use a high-quality septum
1. Leave the GC between 40 to 50 °C for 8 or distance
Ghost Peaks
appropriate for the inlet
granted (“set it and forget it”). The areas and items to temperature Sample degradation in the Reduce the injector temperature If the temperature is too low, peak
more hours. injector broadening or tailing may occur
check include: Contamination of sample before Check sample handling steps for
introduction to the GC potential contamination sources:
Usually occurs after changing
a gas cylinder Change to an on-column injection Requires an on-column injector

2. Run a blank analysis (i.e., start the GC, but with no sample cleanup, handling,
transfer, and storage Poor sample focusing Use a retention gap For splitless and on-column
–– Gases: pressures, carrier gas average linear velocity, injection
injection) using the normal temperature conditions Semivolatile contamination Bake-out column. Solvent Limit bake-out to 1 to 2 hours.
and flow rates (detector, split vent, septum purge) (peak widths will be broader rinse the column. Check for Only for bonded and cross-linked
and instrument settings. than sample peaks with similar contamination in the inlet, phases
retention) carrier gas, or carrier gas lines
Retention Time Shift Possible Cause Solution Comments
–– Temperatures: column, injector, detector, and transfer Change in carrier gas velocity Check the carrier gas velocity All peaks will shift in the same
3. Collect the chromatogram for this blank run. direction by approximately the
lines Excessive Possible Cause Solution Comments 2.00 2.75 same amount

4. Immediately repeat the blank run when the first one Baseline Noise
Injector contamination Clean the injector; replace liner, Try a condensation test; gas lines
4.75 5.50
Change in column temperature Check the column temperature Not all peaks will shift by the same
–– System parameters: purge activation times, detector gold seal may also need cleaning amount
is completed. Do not allow more than 5 minutes to Column contamination Bake out the column Limit the bake-out to 1 to 2 hours 4.00 Change in column dimension Verify column identity Measure the carrier gas velocity
attenuation and range, mass ranges, etc.
3.25
with an unretained compound
elapse before starting the second blank run. Solvent rinse the column Only for bonded and cross-linked
phases Large change in compound Try a different sample May also affect adjacent peaks.

–– Gas lines and traps: cleanliness, leaks, and expiration concentration concentration Sample overloading is corrected
5. Collect the chromatogram for the second blank run Check for inlet contamination with an increase in split ratio or
sample dilution
Detector contamination Clean the detector Usually the noise increases over
–– Injector consumables: septa, liners, O-rings, and and compare it to the first chromatogram. time and not suddenly Leak in the injector Leak check the injector A change in peak size usually also
occurs
ferrules Contaminated or low-quality Use better grade gases; also Usually occurs after changing a
6. If the first chromatogram contains a larger amount gases check for expired Gas Clean
filters
gas cylinder Blockage in a gas line Clean or replace the plugged line More common for the split line;
also check flow controllers and

–– Sample integrity: concentration, degradation, solvent, of peaks and baseline instability, the incoming carrier Column inserted too far into
the detector
Reinstall the column Consult GC manual for proper
insertion distance Septum leak Replace septum
solenoids
Check for needle barb
and storage gas line or the carrier gas is contaminated. Incorrect detector gas flow Adjust the flow rates to the Consult GC manual for proper flow Sample solvent incompatibility Change sample solvent For splitless injection
rates recommended values rates Use a retention gap
–– Syringes: handling technique, leaks, needle sharpness, 7. If both chromatograms contain few peaks or little Leak when using an MS, ECD,
or TCD
Create leak-free column unions
with an UltiMetal Plus Flexible
Usually at the column fittings or
injector
and cleanliness baseline drift, the carrier gas and incoming carrier gas Metal ferrule or a Self Tightening
column nut Change in Peak Size Possible Cause Solution Comments

lines are relatively clean. Old detector filament, lamp, or Replace appropriate part Change in detector response Check gas flows, temperatures, All peaks may not be equally
–– Data system: settings and connections electron multiplier and settings affected

Septum degradation Replace septum For high temperature applications, Check background level or noise May be caused by system
use an appropriate septum contamination and not the detector

View the Agilent GC troubleshooting videos: Change in the split ratio Check split ratio All peaks may not be equally
affected
agilent.com/chem/gctroubleshooting Baseline Instability Possible Cause Solution Comments All Peaks Some Peaks Change in the purge activation Check the purge activation line For splitless injection
time
Injector contamination Clean the injector Try a condensation test; gas lines
For Agilent Technical Support, please visit or Disturbances may also need cleaning Change in injection volume Check the injection technique Injection volumes are not linear
Column contamination Bake out the column Limit a bake-out to 1 to 2 hours
agilent.com/chem/techsupport Unequilibrated detector Allow the detector to stabilize Some detectors may require up to
Change in sample concentration Check and verify sample
concentration
Changes may also be caused
by degradation, evaporation, or
24 hours to fully stabilize variances in sample temperature

Locate supplies and parts with ease: Incompletely conditioned Fully condition the column More critical for trace-level
Leak in the syringe Use a different syringe
or pH
Sample leaks passed the plunger
column analyses
agilent.com/chem/partsfinder Change in carrier gas flow rate Often normal MS, TCD, and ECD respond to
or around the needle; leaks are not
often readily visible
during the temperature program changes in carrier gas flow rate
Find the correct GC column for your application: Column contamination Trim the column Remove 0.5 to 1 meter from the
front of the column

selectgc.chem.agilent.com Fronting Peaks Possible Cause Solution Comments

Column overload
Improper column installation
Agilent GC solutions deliver the highest level of Injection technique
Reduce mass amount of the
analyte to the column.
Decrease injection volume, dilute
sample, increase split ratio
Reinstall the column in the
injector
Change technique
Solvent rinse the column Only for bonded and cross-linked
phases
Most common cause for fronting
Column activity Irreversible Only affects active compounds
peaks
Coelution Change column temperature Decrease column temperature
or stationary phase and check for the appearance of
Consult the GC manual for the a peak shoulder or tail
proper installation distance
Usually related to erratic plunger
Change in injector
discrimination
Maintain the same injector
parameters
Most severe for split injections

analytical performance and day-after-day productivity, Symmetrical Fronting Overload

depression or having sample
in the syringe needle. Use an Sample flashback Use Agilent Vapor Volume
Calculator to adjust injection size,
Less solvent and higher flow rates
are most helpful
autosampler
with the assurance of legendary Agilent reliability and Compound very soluble in Change solvent. Using a retention More critical for trace-level
liner volume, inlet temperature,
or solvent
technical support. injection solvent gap may help analyses
Decomposition from inlet Clean the injector; replace liner, Only use deactivated liners and
Mixed sample solvent Change sample solvent Worse for solvents with large contamination gold seal glass wool in the inlet
differences in polarity or boiling
Learn how Agilent’s innovations in GC provide the points

reliability your lab needs at
www.agilent.com/chem/gcproductivity Tailing Peaks Possible Cause
Column contamination
Column activity
Solvent-phase polarity mismatch Change sample solvent to a
single solvent
Solvent effect violation for
splitless or on-column injections
Too low of a split ratio
Poor column installation
Some active compounds
always tail
This information is subject to change without notice.
© Agilent Technologies, Inc. 2019
Published in the USA, April 15, 2019
5994-0451EN
Solution
Trim the column
Solvent rinse the column
Irreversible. Replace the column
Use a retention gap
Decrease the initial column
temperature
Increase the split ratio
Reinstall the column
Utilize inert flow path
consumable components
(agilent.com/chem/inert)
Comments
Remove 0.5-1 meter from the
front of the column
Only for bonded and cross-linked
phases
Check for inlet contamination
Only affects active compounds
More tailing for the early eluting
peaks or those closest to the
solvent front
3 to 5 meter gap is sufficient
Peak tailing decreases with
retention
Flow from split vent should be
20 mL/min or higher
More tailing for the early eluting
peaks
Most common for amines and
carboxylic acids
Loss of Resolution Possible Cause Solution Comments
Decrease in separation
Different column temperature Check the column temperature Differences in other peaks will be
10.59 10.83 10.59 10.77 10.59 10.77
visible
Separation
Different column dimensions Verify column identity, measure Differences in other peaks will be
or phase the carrier gas velocity visible
Peak
width Coelution with another peak Change column temperature Decrease column temperature
and check for the appearance of
Wh = 0.059 Wh = 0.059 Wh = 0.105
a peak shoulder or tail
R = 2.4 R = 1.5 R = 0.84
Decrease in Increase in Increase in peak width
Separation Peak width
Change in carrier gas velocity Check the carrier gas velocity A change in the retention time
also occurs
Column contamination Trim the column Remove 0.5 to 1 meter from the
front of the column
Solvent rinse the column Only for bonded and cross-linked
phases
Change in the injector Check the injector settings Typical areas: split ratio, liner,
temperature, injection volume
Change in sample concentration Try a different sample Peak widths increase at higher
concentration concentrations
Improper solvent effect, Lower oven temperature, better For splitless injection
lack of focusing solvent, sample phase polarity
match, use a retention gap