Gas Chromatography
Mass Spectrometry
TROUBLESHOOTING GUIDE
Contents
Introduction 04
No Peaks 05
Broad Peaks 06
High Baseline (Column Bleed) 07
Unstable Baseline (Spiking, Noise, Drift) 08
Tailing Peaks 09
Changes in Response 10
Carryover/Ghost Peaks 11
Fronting Peaks 12
Poor Peak Resolution 13
Split Peaks 14
Retention Time Variability 15
Changes in MS Resolution 16
Undesired Fragmentation 17
Shimadzu / Gas Chromatography Mass Spectrometry Troubleshooting Guide
Introduction No Peaks
Instrument downtime is often costly and time consuming, but
frequently the problems can be resolved quickly with some
troubleshooting knowledge.
This Gas Chromatography Mass Spectrometry Troubleshooting Guide is designed to assist
chromatographers assess common GCMS problems. Shimadzu have included how to
effectively troubleshoot and fix these issues to allow you to get your system back up and
running and continue your analyses.
Basic Steps
Follow these three steps to isolate the source of the problems. Check the obvious causes Causes Solutions
first and change only one thing at a time! Injection problems - Blocked syringe; clean or replace syringe.
- Verify there is sample in the vial.
Check the Basics: - Injecting into wrong inlet; reset autosampler.
• Power supply • Temperature settings - Verify carrier gas is flowing.
• Electrical connections • Gas purity Broken column - Replace column.
• Signal connections • Gas flows
Column installed into - Reinstall column.
• Syringe condition • MS vacuum
wrong inlet or detector
• Sample preparation • Collision gas (level & pressure)
• Analytical conditions • Rough pump (oil level & gas ballast) Detector problems - Ensure MS is an appropriate technique for the analyte(s)
- Check the vacuum is sufficient and stable, perform
a leak check.
Identify the Cause: Document Everything:
- Perform and check the MS tune.
• Define the problem clearly; for • Document all troubleshooting steps and
- Check the ion source temperatures and gas flows are as
example, “Over the last four days, results; this may help you identify and
expected and stable.
only the phenols in my sample have solve the next problem faster.
been tailing.” - Check the collision gas pressure is correct and stable.
• Always inject a test mix and compare
• Review sample and maintenance to previous data to ensure restored - If the method contains scheduled events, such as MRM,
records to identify trends in the data performance. ensure the analyte elutes within the correct event window.
or problem indicators, such as area - Check that the concentration of the analyte is above the
counts decreasing over time or inlet Still having problems? limit of detection.
maintenance not being performed
Still struggling? Let us know!!! - Blown filament, switch to second filament and replace the
as scheduled.
[email protected] first as soon as practicable.
• Use a logical sequence of steps to
isolate possible causes.
04 05
Shimadzu / Gas Chromatography Mass Spectrometry Troubleshooting Guide
Broad Peaks High Baseline
(Column Bleed)
Causes Solutions
Causes Solutions
High dead volume - Minimise dead volume in the GC system; verify proper
column installation, proper connectors, proper liners, etc. Improper column - Increase conditioning time and/or temperature.
conditioning
Low flow rates - Verify carrier gas flow rate and adjust if needed.
Contamination - Trim column and/or heat to maximum temperature to
Slow GC oven program - Increase GC oven programming rate.
remove contaminants.
Poor analyte / solvent - Lower GC oven start temperature. - Replace carrier gas and/or detector gas filters.
focusing - Clean injector and ion source.
Column film is too thick - Reduce retention of compounds by decreasing film Leak in system - Check for oxygen leaks across the entire system and
thickness and length. causing oxidation of replace seals and/or filters. Perform a manual tune and
Sample carryover - See Carryover/Ghost Peaks solutions. stationary phase look for the presence of m/z 18, 28 & 32. Large peaks
will indicate a leak.
- Check the column fittings on the inlet and MS transfer line.
- Replace column.
- Check the seal around the access door to the MS.
06 07
Shimadzu / Gas Chromatography Mass Spectrometry Troubleshooting Guide
Unstable Baseline Tailing Peaks
(Spiking, Noise, Drift)
Spiking Noise Drift
Causes Solutions
Causes Solutions
Adsorption due to surface - Use properly cleaned and deactivated liner and column.
Carrier gas leak or - Leak check the system and check that the flow and activity or contamination - Trim inlet end of column.
contamination pressure controllers are functioning correctly.
- Replace column if damaged.
- Replace carrier gas and/or detector gas filters.
Adsorption due to - Derivatise compound.
Inlet or detector - Clean the inlet and ion source. Schedule and perform
chemical composition of
contamination regular maintenance. compound
Column contamination - Condition, trim, and rinse column. Leak in system - Check for leaks at all connections, replace critical
or stationary phase bleed
seals if needed.
Septum coring / bleed - Replace septum.
Column installation - Minimise dead volume.
- Inspect inlet liner for septa particles and replace if needed. issues - Verify correct installation depth.
- Replace the solvent in the wash vials.
- Verify that the column is cut properly (square).
- Perform a manual tune, the presence of m/z 73, 147,
207, 281 & 355 will indicate siloxane contamination from
damaged septa.
Aging filament - Switch to second filament and replace the first as soon as
practicable.
Variable carrier gas - Leak check the system and check that the flow and pressure
or detector gas flows controllers are functioning correctly.
- Check collision gas pressure.
Detector not ready - Allow enough time for ion source and transfer line
temperatures to equilibrate.
08 09
Shimadzu / Gas Chromatography Mass Spectrometry Troubleshooting Guide
Changes in Response Carryover/Ghost Peaks
Injection 1 Injection 2
Causes Solutions
Sample issues - Check sample concentration. Causes Solutions
- Check sample preparation procedure. Contaminated syringe - Replace rinse solvent.
- Check sample decomposition/shelf life. or rinse solvent - Rinse or replace syringe.
Syringe problems - Replace syringe. Backflash (sample - Inject a smaller amount.
- Check autosampler operation. volume exceeds - Use a liner with a large internal diameter.
liner volume)
Electronics - Verify signal settings and adjust if needed. - Increase head pressure (i.e. flowrate) to contain
the vapour cloud.
Dirty or damaged - Clean the ion source and replace the electron multiplier if
- Use slower injection rate.
detector required.
- Lower inlet temperature.
- Check and replace filaments if required.
- Use liner with packing.
Flow / temperature - Verify steady flow rates and temperatures, then adjust - Use pressure-pulse injection.
settings wrong or variable settings and/or replace parts if needed. - Use online calculator to check expansion volume.
Adsorption / reactivity - Remove contamination and use properly deactivated liner Last analysis ended - Extend analysis time to allow all components and/or matrix
and column. too soon interferences to elute.
Leaks - Check for leaks at all connections and repair connections
as needed.
Change in sample - Verify injection technique and change back to
introduction / injection original technique.
method - Check that split ratio is correct.
- Verify that the splitless hold time is correct.
10 11
Shimadzu / Gas Chromatography Mass Spectrometry Troubleshooting Guide
Fronting Peaks Poor Peak Resolution
Causes Solutions
Causes Solutions Non-selective stationary - Choose an appropriate stationary phase and column
phase dimensions.
Incompatible stationary - Choose appropriate stationary phase.
phase Poor efficiency - Optimise carrier gas linear velocity and GC oven
Column overloading - Reduce amount injected, dilute sample or increase temperature program.
split ratio. Sample overload - Adjust sample concentration or amount on column by
- Increase column inner diameter and/or film thickness. increasing split ratio.
Incorrect analytical - Verify temperature program, flow rates, and column
conditions used parameters.
MS method - Use different m/z when using selected ion monitoring
settings (SIM) or a different transition in multiple reaction
monitoring (MRM).
- Set quadrupole to ‘High’ resolution for analytes affected
in MRM mode.
12 13
Shimadzu / Gas Chromatography Mass Spectrometry Troubleshooting Guide
Split Peaks Retention Time Variability
Causes Solutions Causes Solutions
Mismatched solvent / - Adjust solvent or stationary phase to allow wetting. Leaks - Leak check inlet and any column connections.
stationary phase polarity - Replace septa, O-rings, etc.
Incomplete vaporisation - Add surface area, such as wool, to the inlet liner to enhance Analyte adsorption - Maintain inlet liner and GC column.
vaporisation. - Use properly deactivated liners and columns.
- Use proper inlet temperature.
Resolution / integration - Avoid sample overload by diluting sample or increasing
Sample loading capacity - Inject less sample (dilute, use split injection, reduce injection issues split ratio.
exceeded volume).
Incorrect column / oven - Verify column temperature and oven temperature program.
Fast autosampler - Use wool or slow injection speed. temperature program
injection into open liner
Incorrect or variable - Verify the carrier gas linear velocity.
Detector saturation - Reduce the injection volume or inject a lower concentration carrier gas linear velocity - Repair or replace parts if necessary.
of sample.
- Set quadrupoles to ‘High’ resolution for analytes affected in Poor control of - Confirm GC oven program falls within
MRM mode. oven temperature instrument specifications.
programming
Incorrect oven - Extend GC oven equilibration time.
equilibration time
If manual injection, - Use autosampler or standardise manual injection procedure.
inconsistencies between
pushing start and
injection procedure
14 15
Shimadzu / Gas Chromatography Mass Spectrometry Troubleshooting Guide
Changes in MS Resolution Undesired Fragmentation
Causes Solutions Causes Solutions
MS out of tune - Perform and check tune Ion source setting - Check source temperatures are appropriate for the analyte.
too harsh - Check ionisation voltage is appropriate for the analyte.
Collision energy too - Check and optimise the collision cell gas pressure
low / high and collision energy.
Aging filament - Change to the second filament and replace the first as
soon as practicable.
Contaminated source - Clean the ion source and perform a tune.
16 17
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