TROUBLE-
SHOOTING
Quick Reference Guide to Troubleshooting Your
GUIDE Gas Chromatography
Introduction Table of Contents
Even with robust preventative maintenance practices Description of the Problem
and schedules in place, sometimes problems appear Poor Compound Resolution................................................2
that affect data quality and need to be resolved as High Column Bleed...............................................................3
quickly as possible.
Peak Tailing...........................................................................4
The first step to being able to solve problems quicky Peak Fronting........................................................................5
is to be able to effectively describe them in the first Excessive Noise....................................................................6
place. Once you can define the nature of the problem,
Signal Spiking........................................................................7
you can begin to seek the solution.
Retention Time Drift.............................................................8
The data itself is often the best source of information Inconsistent Peak Area........................................................9
about what might be wrong. The shape of a peak or Sample Carryover, Contamination and Ghost Peaks.......10
the baseline can direct troubleshooting efforts, and
Split Peaks...........................................................................11
this guide relates those chromatographic clues with
Excessive Band Broadening...............................................12
their probable causes. It also includes tips to consider
when deciding if your preventative maintenance Irregular Baseline................................................................13
program could be updated to stop a problem from Baseline Shift After Dead Time.........................................14
occurring in the first place.
GC Troubleshooting Guide
Poor Compound Resolution
What is Happening?
The selectivity parameter of the analytical system is insufficient to separate two (or more) co-eluting compounds. Their signals
overlap and quantitation becomes difficult. If these compounds are target analytes, they become known as a “critical pair”.
Causes Fixes
Insufficiently optimized analytical method conditions, • Adjust oven temperature program conditions
i.e., low efficiency/plate count
• Adjust linear velocity of the carrier gas
• Seek alternate stationary phase chemistry that better exploits differences between
co-eluting compounds
Column is not suitable for separation
• Seek alternate column dimensions that better targets the chemicals’ volatilities
• If column is old/degraded, a new one may need to be purchased
• Sample needs to be diluted and re-tested
Sample capacity is overloaded • Smaller injection volume is necessary
• Seek alternate column with a wider bore size
Preventative Maintenance
Identify critical pairs in your laboratory’s analytical methods;
ensure appropriate suitability tests are incorporated into
your laboratory workflow to monitor separation efficiency of
critical pairs over time.
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GC Troubleshooting Guide
High Column Bleed
What is Happening?
The column’s stationary phase and/or its degradation byproducts are being flushed out by carrier gas. The result is increased
background and decreased signal/noise ratio that diminishes analytical performance, lowers column lifespan, and shifts
compound retention over time.
Causes Fixes
Column was not properly conditioned prior to use • Condition the column for a longer time and raise maximum conditioning temperature
to maximum allowable
• Leak check connections at the injector with electronic leak detector
A leak in the system is allowing oxygen into the column, • Perform full injector port maintenance
thereby causing stationary phase degradation
• Replace inlet septum
• Replace oxygen filter on your carrier gas cylinder
Column was not properly purged with carrier gas prior • Purge column at room temperature prior to use to remove oxygen from system
to use, thereby causing stationary phase degradation • Purge column at maximum isothermal temperature for 2 hours to remove any
contamination present in column
Preventative Maintenance
Ensure robust column conditioning and purging practices
are adhered to; consult the “PerkinElmer Elite Series®
GC Capillary Column Installation Quick Care Guide” as a
reference. Additionally, incorporate routine leak checks into
laboratory workflows.
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GC Troubleshooting Guide
Peak Tailing
What is Happening?
Compounds have not traveled through the system following a Gaussian distribution, with a bias towards extra retention/
dwell time. These peaks lack robustness in quantitation, readily suffering from poor sensitivity and resolution with neighboring
compounds. Be sure to note if all peaks are tailing or just some, e.g., the most active compounds.
Causes Fixes
Activated inner column surface is causing adsorption
• Trim inlet end of column
of certain compounds • Replace column if damage is extensive
• Perform method at higher temperature if possible
Activated injector port surface is causing adsorption of • Replace septum, inlet liner, and/or gold seal
certain compounds
• Perform full injector port maintenance
Compound is too active for gas chromatography • Chemically derivatize compound if possible
• Ensure column protrudes the correct length beyond the ferrule into both injector port
Column isn’t installed properly (all peaks will tail) and detector
• Ensure the column is cut flatly and without jagged edges
Significant leak in system • Leak check connections at the injector
Preventative Maintenance
Ensure routine injector port maintenance schedules are
adhered to. Ensure proper column handling protocols are
established that include installation, purging, leak checking,
and never heating without carrier gas flow.
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GC Troubleshooting Guide
Peak Fronting
What is Happening?
Compounds have not traveled through the system following a Gaussian distribution, with a bias towards lesser retention/dwell
time. These peaks lack robustness in quantitation, readily suffering from poor resolution with neighboring compounds.
Causes Fixes
• Ensure a smaller compound mass-on-column by adjusting the injection volume, split
ratio, or by diluting the sample
Column is overloaded with sample
• If large sample volumes are necessary, switch to a wider bore column whilst
maintaining the appropriate phase ratio, β, to preserve performance; for reference,
consult the PerkinElmer GC Column Selection Guide
Compound and stationary phase are incompatible • Consult reference materials to determine appropriate stationary phase for your
analytes of interest; switch columns
Preventative Maintenance
To understand the limits of what can be injected without
overloading the column, prepare a series of standards
exploring your system’s entire linear range.
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GC Troubleshooting Guide
Excessive Noise
What is Happening?
Rather than a flat baseline, the signal from the detector rapidly fluctuates to the extent that it lowers the robustness of the
analysis and/or the ability to decipher signal from noise.
Causes Fixes
• Perform full injector port maintenance and replace consumables
System contamination • Bake out column for 2 hours at maximum isothermal temperature
• Perform full detector maintenance and replace consumables
Inlet septum overheated • Ensure that your inlet septum is appropriately suited to your method temperature;
replace if necessary
• Upgrade to ultra-high purity gasses from a trusted vendor
Carrier/detector gasses are of low quality • Replace your moisture/oxygen/hydrocarbon traps if expiredy
• Replace near-empty tank with a fresh one
Column is installed too deeply into detector • Ensure column protrudes the correct length beyond the ferrule into detector
Preventative Maintenance
Schedule and maintain records of routine injector port,
detector, and gas tank servicing.
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GC Troubleshooting Guide
Signal Spiking
What is Happening?
Rather than a flat baseline, the signal from the detector instantly jumps up or down with a near-zero width of each electrical spike.
Causes Fixes
Loose electrical cable • Verify electrical connections in instrument
Electrical noise from detector • Verify all connections (e.g., pins, wires) are positioned correctly with no short circuits
• Replace consumables (e.g., jet, filament) if applicable
Dust buildup • Clean the motherboard and/or detector assembly
Detector was physically jostled • Set up instrument on a sturdy table
• Ensure the instrument and table are not jostled during the analytical run
Particles of stationary phase are entering the detector • Replace the PLOT column
(PLOT columns only)
• Use a particle trap
Preventative Maintenance
Make sure the instrument is placed upon a sturdy table. If
possible, avoid placing instrument adjacent to busy egress
routes to avoid bumping.
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GC Troubleshooting Guide
Retention Time Drift
What is Happening?
A compound’s retention time is changing run-to-run. This shift can occur either suddenly or progressively with time.
Causes Fixes
Column is overloaded with sample • Ensure a smaller compound mass-on-column by adjusting the injection volume, split
ratio, or by diluting the sample
Significant leak in system • Leak check connections at the injector port
Manual injection user error • Practice manual injection so that method start time and sample injection time
are aligned
• Ensure the correct oven temperature program is used
Incorrect oven temperature
• Verify the oven temperature is being properly controlled by the instrument, e.g.,
not too fast a ramp
Column has been trimmed • If possible, adjust analytical method to reflect reduced column length
Stationary phase has bled out over time • Replace column if damage is extensive
Activated inner column and/or injector port surface is • Trim inlet end of column
causing adsorption of certain compounds
• Replace column and/or injector consumables if damage is extensive
Preventative Maintenance
Thoroughly condition each new column prior to use to
guarantee the longest lifespan and most robust retention
times. Do not exceed the thermal limit of your column while
in operation.
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GC Troubleshooting Guide
Inconsistent Peak Area
What is Happening?
A compound’s peak area response is changing run-to-run, thereby altering the response/calibration factor. This shift can occur
either suddenly or progressively with time.
Causes Fixes
Detector response is changing • Check gas flows to the detector
• Check detector settings (e.g., ion source potential, attenuation)
• Check split flow
• Confirm sample concentration and injection volume are that which you expect
Less/more compound is being loaded on-column • Gas saver engaged too early during sample loading
• Confirm syringe isn’t leaking and/or bubbles are not present in sample
• Manual injection only: practice technique for consistency
Activated inner column and/or injector port surface is • Trim inlet end of column
causing adsorption of certain compounds
• Replace column and/or injector consumables if damage is extensive
Sample is undergoing “flashback” within injector • Use less solvent and/or a higher flow rate
• Use a larger-volume liner if available, particularly one with glass wool packing
Preventative Maintenance
Routine injector port and autosampler maintenance and
the adherence to method-defined parameters such as split
flow and detector attenuation are essential for producing
consistent results.
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GC Troubleshooting Guide
Sample Carryover, Contamination and Ghost Peaks
What is Happening?
Chemicals are present in the system (sample and/or instrument) that interfere with the analysis and reduce method robustness.
Causes Fixes
Contaminants are in sample and/or solvent • Ensure all solvents used are chromatography-grade
• Ensure sample handling does not introduce contamination
Not all compounds elute during analytical run, eluting
• Bake out column and injection port for 2 hrs
instead in subsequent run(s) • Lengthen method runtime and increase max temperature if possible
• "Solvent rinse" the column by injecting blank solvent multiple times
• Replace inlet septum to stop septum bleed
Contaminants are in the injector port • Replace syringe and autosampler wash solvent
• Perform full injector port maintenance and replace consumables
• Use less solvent and/or a higher column & split flow rates
Sample is undergoing “flashback” within injector port • Lower injection port temperature
• Use a larger-volume liner if available, particularly one with glass wool packing
Preventative Maintenance
Ensure method parameters are thoroughly vetted and
maintained, including suppliers of solvents & standards.
When a new sample matrix is explored, always first
lengthen the analysis time and raise column to the
maximum operating temperature to allow elution of
potential contaminants.
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GC Troubleshooting Guide
Split Peaks
What is Happening?
Compounds are moving through the column not as a discrete band, but as two bands with near-eluting maxima.
Causes Fixes
• Use a glass wool-filled liner to aid in the flash-vaporization of sample
Inlet liner isn’t focusing properly • Use a slower syringe injection speed
• Use an injector temperature that is suited for your sample solvent and analytes
of interest
A mixed-solvent system with incompatible solvents is • Change solvent system to either a single solvent or to two solvents with more similar
being used boiling points and/or polarities
• Switch to a deactivated liner if possible
Sample is degrading within the injector port • Reduce injector port temperature
• Use on-column injection if possible
Column is not installed properly within the injector • Re-install the column according to manufacturer specifications
Incompatibility between solvent and stationary phase • Build your method around a different solvent system
Preventative Maintenance
Establish and maintain a routine schedule to examine/replace
the inlet liner. Ensure the method, especially the solvent
system, is properly validated.
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GC Troubleshooting Guide
Excessive Band Broadening
What is Happening?
Peaks are wider, and therefore shorter. This can have the effect of reducing the sensitivity of analysis and resolution with
near-eluting compounds.
Causes Fixes
• Lower oven starting temperature/slow temperature programming rate
Sample is not being properly focused at the head of • Increase split flow
the column • Ensure sample is not undergoing “flashback” within injection port; reduce sample
volume or use larger volume liner
• In headspace analysis, decrease injection time
Carrier gas flow rate is too low • Adjust column flow rate as needed
Column dimensions are not suited for analyte • Use a shorter column
• Use a thinner film column
Peak is resultant from sample carryover • See section on carryover
Preventative Maintenance
Validate each analytical method and strictly adhere to the
method parameters.
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GC Troubleshooting Guide
Irregular Baseline
A compound’s peak area response is changing run-to-run, thereby altering the response/calibration factor. This shift can occur
either suddenly or progressively with time.
Causes Fixes
Detector hasn’t equilibrated • Upload method conditions to the instrument and wait for the baseline to stabilize
• Perform a blank solvent injection
Column hasn’t been conditioned properly • Perform column conditioning according to the “PerkinElmer Elite Series® GC
Capillary Column Installation Quick Care Guide”
Carrier gas flow rate • Ensure gas cylinder utilizes a high quality two-stage regulator
• Decrease carrier flow rate
House gas generator has a pressure cycle time • Use ultra-high purity gas from a cylinder
Preventative Maintenance
If an instrument is used daily, it is often best to keep
flow through the column overnight, rather than turning it
off, to mitigate the effects of detector equilibration. Fully
characterize the performance of your method on each gas
source as a validation step.
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GC Troubleshooting Guide
Baseline Shift After Dead Time
After elution of the solvent peak the baseline undergoes a semi-permanent shift upwards or downwards for the remainder of the run.
Causes Fixes
Septum cannot maintain gas-tight seal at inlet • Replace inlet septum
Preventative Maintenance
Manufacturers recommend frequent replacement of
the inlet septum to ensure system isolation from the
outside environment. Build septum replacement into your
servicing schedule.
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