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Troubleshooting
Tips & Tricks for
your GC Analyzer &
CFT Application

7890 Detectors

October 29, 2014

1
Detector Types

Flame Ionization Detector (FID)

Thermal Conductivity Detector (TCD)
Electron Capture Detector (µECD)
Nitrogen-Phosphorous Detector (NPD)
Flame Photometric Detector (FPD)
Photo Ionization Detector (PID)
Electrolytic Conductivity Detector (ELCD)
Infrared Detector (IRD)
Mass Selective Detector (MSD) Items in red covered in this course
Agilent 7890 FID Theory of Operation

H2 – Air Flame
Sample is burned in
flame.
Charged Ions
produced.
Ions attracted to
collector.
Collector current
converted to output
via Electrometer.
FID Problem #1

#6

#9
#7
#8
#3
#2
#1

#5
#4
Before After
Normal

Peak Peak Peak Before After

No. Width Width Area Area Type

#1 0.014 0.102 288 6213 TBB

#2 0.020 0.111 559 2922 TBB
#3 0.022 738 BB
#4 0.026 0.024 585 227 BV
#5 0.025 267 VB
#1

#6 0.029 0.030 1231 543 BB

#2

#7 0.035 0.036 1010 396 BB

#8 0.030 1041 BV
Problem

#6
#7

#9
#4

#9 0.031 0.031 1195 478 BB

FID Problem #2

#1

#9
#2

#5

#7
#4
#3

#8
#6
Before After
Normal

Peak Peak Peak Before After

No. Width Width Area Area Type

#1 0.014 0.031 288 259 BB

#2 0.020 0.020 559 503 BB
#3 0.022 0.022 738 664 BB
#4 0.026 0.026 585 526 BV
#5 0.025 0.024 267 240 VB
#6 0.029 0.028 1231 1170 BB
#9
#6
#7
#1

#8
#2

#5
#4
#3

#7 0.035 0.034 1010 909 BB

Problem

#8 0.030 0.030 1041 936 BV

#9 0.031 0.030 1195 1075 BB
Agilent 7890 FID Jets
Adaptable FID Jets
Jet Type Part# Jet Tip ID

0.29 mm
Capillary 19244-80560
0.011 in.

0.47 mm
Packed 18710-20119
0.018 in.
0.79 mm
Paced Wide Bore 18789-80070
0.030 in.
0.47 mm
High Temp G1531-80620
0.018 in.

Capillary-Optimized FID Jets

Jet Type Part# Jet Tip ID
0.29 mm
Capillary G1531-80560
0.011 in.

0.47 mm
High Temp G1531-80620
0.018 in.
Agilent 7890 FID Setup – Column Installation
General Rule:
Push to tip of Jet
then withdraw 1 mm.

Capillary Optimized FID Adaptable FID

0 10 20 30 40 50

mm
0 10 20
mm

48mm
68mm 1mm
30 40 50 60 70
Exploded Parts View of the FID
Agilent 7890 FID EPC Flow Module
FID EPC Module
Agilent 7890 Flame Ionization Detector

Typical Problems
• Flame blowing out or not lighting

• Spiking

• Low Sensitivity

• Noise

• Drift
Solving FID Lighting Problems

Check detector parameter settings (keyboard).

• Flows
• Flame on
• Detector on
• Lit offset
Check jet.
Check igniter.
Check column connections.
Check gas supply pressures.
Check solvent and injection size.
Solving FID Noise Problems
Turn off
H2 and Air.

Yes Still No
Noisy?

Check/Clean/Replace: Check/Clean/Replace:
•Interconnect/collector connection. •Filters, traps, gases.
•Collector and insulators. •FID jet.
•Detector interconnect. •Column and connections.
•Detector board. •Inlet and consumables.

Electrical Problem. Contamination Problem.

Routine FID Maintenance
Monitor the background signal.
Check pressures/flows.
Clean or replace the jet.
Inspect the igniter assembly.
Clean the collector assembly.
Remove, trim and reinstall column.
Agilent 7890 Flame Lighting Problems

Check the following:

Measure flows.

Clean/replace jet.

Are column and fittings tight?

Do we have supply gases?

Is detector on?
Agilent 7890 Thermal Conductivity Detector

Thermal Conductivity Values of Common Gases/Solvents

Compound Relative Thermal Conductivity

Carbon Tetrachloride 0.05

Benzene 0.11

Hexane 0.12
Argon 0.12
Methanol 0.13
Nitrogen 0.17
Helium 1.00
Hydrogen 1.28

Thermal Conductivity Relative to Helium

Thermal Conductivity Basics
The TCD is a nondestructive, When the carrier gas is contaminated
concentration sensing detector. by sample , the cooling effect of
A heated filament is cooled by the gas changes. The difference in
the flow of carrier gas . cooling is used to generate the detector
signal.
Flow

Flow
The TCD will respond to any substance different
from the carrier gas as long as its concentration is
sufficiently high enough.
Agilent 7890 TCD 5 Hertz Pneumatic Switching

COLUMN flow enters the center of

three ports.

REFERENCE flow is directed to either

one of the outside ports into the
detector cell. The port entered is
determined by the SWITCHING
SOLENOID.

AUXILIARY, or makeup, flow passes

along the outside of the column and
merges with the column flow prior to
entering the detector’s center port.
TCD Normal Flow Ratio

20 mL/min
Col + MUG 30 mL/min
Reference Sample
Filament

Filament
+ Reference
10 mL/min Ref
Reading Reading

20 mL/min
Reference 20 mL/min
Col + MUG

30 mL/min 30 mL/min
Reference 20 mL/min 20 mL/min Reference
Column + MUG Column + MUG

Signal (+ polarity) = Sample - Reference

TCD Problem #1

#6
#3

#8
#2

#9
#7
#4
#5
#1
Before After
Normal

Peak Peak Peak Before After

No. Width Width Area Area Type

#1 0.030 0.028 1920 1643 BB

#2 0.033 0.031 4279 3215 BB
#3 0.028 0.027 4503 3803 BB
#4 0.033 0.031 3380 3043 BV
#8 #5 0.026 0.023 2109 1810 VB
#3

#6

#6 BB
#2

#9 0.038 0.036 7233 6528

#7

#7 0.044 0.040 4386 3551 BV

#4
#5
#1

#8 0.046 0.043 6898 6124 VB

Problem

#9 0.050 0.049 6817 6252 BB

Choosing Reference Flow Rate
Ratio of Ref flow to Column + MUG

3.5

2.5

1.5

0.5
0 5 10 15 20 25 30 35 40 45 50 55 60 65 70

Column + Makeup flow (mL/min)

Column + MUG Flow = 10 mL/min

Ref flow = 2.3 X 10 = 23 mL/min
Agilent 7890 TCD EPC Flow Diagram
Agilent 7890 TCD EPC Module
Reference Gas Line

Switching Valve

Make Up Gas Line

Agilent 7890 TCD Filament Drive – ΔT Sensor
500 DT 50C
400

Response Filament 300

Temp C
200
DT135C
100

100 200 300 400 100 200 300 400

Detector Temp (body temp) C
Detector response versus detector temperature. Filament Temperature versus Block Temperature.
TCD Typical Problems
Drifting or wandering baseline
• Normal in temperature programmed analysis
• Check heaters/sensors.
• Remove contamination by thermal cleaning the detector.

Low sensitivity
• Check gas flows.
• Check column installation.
• Contamination – thermal clean the detector.

Elevated background signal or increased noise level

• Contamination – thermal clean

Conditions that prevent the detector from operating

• Temperature set below 100°C
• Broken or shorted filament
• Reference gas flow set to 0
Valves
What are Valves?

Valves are mechanical devices used to switch gas streams.

They are the pneumatic equivalent to the electrical switch.
4 Port LSV with Internal Sample Volume
Gas Tight Syringe versus Gas Valve Injection

Typical values for valve injection reproducibility is <0.5% RSD.

Typical values for manual gas tight syringe injection reproducibility is <5.0%
RSD.

Multiple valves can be filled in series with a gas sample.

Manual syringe can only fill 1 injector port.

Note for small sample volumes (<2mL) can only use gas tight syringe.
Injection with Gas Sampling Valves

Loop of known volume switched into carrier gas stream.

Factors that affect the amount of sample transferred onto the column:

• PV=nRT
- Temp = temperature of valve box
- R = ideal gas constant
- V= volume of sample loop

Pressure is proportional to the amount of mole of gas within sample

loop.
How Are Gas Samples Injected?

Gas sampling valves are the most common way of sampling a

gas and are used in almost all cases on bench top GC’s.

Almost all gas sampling valves installed on GC’s are produced

by VICI™. Spare valve parts can be ordered directly from VICI
if required.
www.vici.com

Gas tight syringes can also be used for injection but they are
not as reproducible and are more cumbersome.
In This Section, We Will Discuss:
Valve rotor replacement
Problems associated with valve GCs
Dealing with water vapor
Backflushing
Reconditioning mol sieve columns
Nafion driers
Genie membrane filter
Trace sulfur gases
SCD potential problems
Other problem compounds
Gas Sample Valves
Liquid Sample Valves
Valve Timing
Valve Rotor Replacement

Number of ports ID letter toward

3 Port 2
4 Port 3
6 Port 4
8 Port 5
10 Port 6
Problems Associated with Valve GC’s
-Moisture is far more important when you are using columns who performance will drop
dramatically with moisture absorption.

-Many valved GC’s will have at least 1 x Molecular Sieve column installed so water
handling is very important.

-The system should be designed to restrict moisture from reaching these columns from
the sample (there are rare exceptions to this).

-Carrier gas is typically at volume of at least 1000 times that of the sample throughout the
period of day so it’s dryness is absolutely critical (indicating moisture filters must be used).

- In many cases the sample is not visible before it is connected to the GC so

contamination of GSV lines with liquid or metal particles (especially the later) can cause
immediate damage.

-Use an inline filter wherever possible to minimize sample impact to system.

Dealing with Water Vapor
Benchtop GC
Water can be chromatographed and analyzed but this is not
recommended.

• Problems with preparation of accurate standards

• Poor peak shape

• Memory effects

• On non polar columns it appears as very broad peak which can interfere
with other components (RT can shift dramatically too)

It is possible to analyze on polar columns.

Dealing with Water Vapor (cont.)

PROBLEMS

If sample gas stream is saturated with moisture then

condensation can occur on cold internal tubing surfaces and
cause loss of analytes and other more serious problems.

Absorbed onto Molecular Sieve columns deactivating them,

thus less retention and separation of components.

Absorbed onto Alumina columns with resulting shifting in RT’s.

Backflushing

In many cases it is possible to backflush water from the sample

to Vent.

This option is available on either the Micro GC or Bench top GC

unit.

Backflushing of water is only possible if analytical compound

elutes before C3, as water will typically elute between C2 and
C3 on most columns.
Backflush Micro GC
Sample in

injector

CP-Sil 5 CB
µ-TCD µ-TCD µ-TCD µ-TCD
Backflushing - Bench Top Unit

0.5m Hayesep N columns used for backflush of water.

Loss of Resolution Due to H2O Absorption
Reconditioning Molecular Sieve Columns
Molecular Sieve columns can be reconditioned.

• Bench top GC
- heat Molecular Sieve column to 300°C for a minimum of 4 hours.

• Micro GC
- heat 180°C, pressure 45psi O/N minimum

NOTE:

• Remove any other columns from GC oven not suited to temperature, replace
with empty ss column.

• Must turn off TCD filaments and ensure carrier gas is dry during
reconditioning.
Removing Water Vapor

There are many ways to remove moisture from your samples

prior to analysis.

Condensing - run sample through cooler with collecting coil.

Desiccants - may alter conc. of other analytes)

Nafion Dryer - a good solution but can result in the loss of

some amount of some polar analytes such as methanol.
Nafion Dryers

• Wet feed gas in

• Dry purge gas, typically at
min of 10x sample flow in
opposite direction
• Dry feed gas to analyzer
http://www.permapure.com/
Nafion Dryers

• Nafion is a special extremely

hydroscopic membrane type
material.
• Allows easy removal of moisture
with little if any alternation to
sample.
• Highly recommended for Micro GC
applications.
• Also useful for bench top.
Genie Membrane Filter
Removes droplets – only • Protects the analyzer from damage and contamination
required for µGC
• Fully inert membrane technology

• Proven and widely accepted filtering technique

• Removes liquids from gas samples

• Removes particles from gas samples

• No interference with sample composition

• Compliant for BTU calorific value applications

• Suitable for PPB, PPM and percentage level analysis

• Standard Swagelok™ connections

• High and low flow membranes

Genie Model 170
• Stainless Steel, Polypropylene and Kynar housing

• Standard Viton housing seal

Moisture from Sample or Carrier Gas
Remember moisture from carrier gas is far more susceptible to cause problems with
columns and BF will not remove.

On a Micro GC, typical column flow 2mL/min.

Typical sample Introduction volume is 200nL.

If you inject one sample every 5 min(s) total sample volume introduced, 2400nL.

In 1 hour you have 120 mL of carrier gas through your column, so the moisture
content of your carrier gas is 50,000 times more important than your sample gas.

Always use a carrier gas filter with certain types of packed columns.
Trace Sulfur Gases
Low level sulfur analysis requires the following:

•Inert surfaces at every point.

•Accurate standard(s)
• Shelf lifetime is limited due to reactivity of sulfur components (consider Dynacalibrators).

•Agilent uses Hastelloy C Valves with all sample path material including the
detector in Ultimetal.

•Use the most inert stationary phase where possible, CP-Sil5CB.

Trace Sulfur Gases

•H2S, SO2, COS are the most reactive components, with

CH3SH, EtSH and on being increasingly less reactive.

•RSD’s for reproducibility typically 3-5% for H2S, SO2 and

COS, 5-10% for SO2 maybe 1-3% for other sulfur
components.
Percent Level Sulfur Determination

High levels of sulfur species >0.1% should not be analyzed on

a FPD due to linear range issues but instead on a TCD.

Use a small loop size to limit impact on corrosive sulfur species

generated by reaction of sulfur components with moisture on
filaments in TCD.

Dry sample stream if it contains appreciable amounts of

moisture and sulfur species such as SO2, H2S, etc.
SCD Potential Problems

•High maintenance detector, vacuum pump, ozone generator

etc.

•Ceramic tubes can easily become contaminated and need

replacement.

• indication through loss of sensitivity,

• thick film methyl silicone columns can cause this if heated to

higher temperatures
Other Problem Compounds

•Chlorine

•Ammonia, if not to be analyzed can be removed using an acid

solution with a pH indicator present.

•Special columns designed for ammonia analysis.

• Volamine or Chromosorb 103

•No ammonia analysis by µGC.

Sample Introduction Systems (Problems)

Bench Top

• Gas Sampling Valve

• Liquid Sampling Valve
• Injector Port

Micro GC

• Specific injection technique

Gas Sampling valves

Valve cores are rated for different temperature ranges.

• Ambient - 175°C
• 100-300°C
• ambient to 225°C (valcon E)

Do not overheat or they will no longer function correctly!

Gas Sampling Valves-6 Port
Valves - WCGW

•Valve core damaged due to overheating.

•Valve core scratched- gives leaks.
• Use Inline filters to stop this occurring
•Valve core or channels blocked.
•Loop blocked
•Leaks at fittings although this is unlikely.
•Always use correct Valco ferrules and nuts.

Replace valve core and body as one unit, carry a spare if

at all possible.
Valves- WCGW

Actuators may not turn

• Insufficient gas pressure or not on, require 60psi

Actuators may not be aligned correctly

• incorrect removal from valve

Wrong angle actuator

• check degree turn
• Agilent actuators versus other actuators

Micro Electric Actuators

Liquid Sampling Valves

Fixed volume - internal groove -1µl

Liquid must be under pressure to remain in liquid phase.

Easily blocked - use filters to remove particles before the

sample inlet.

Use apparatus as described (drawing) for ensuring liquefied

gas remains in liquid state.
Sample Introduction Devices
Gas (Refinery gas, Natural gas)
• Pressure
Sample
• 1015 PSI for Natural gas treatment
• Up to 290 PSI for Refinery gas

Controlled pressure reduction

Why
• Max 45 PSI sample inlet pressure for bench GCs and max 15 PSI
for the 490 Micro-GC Controlled sample flush flow.
• Constant sample pressure prior injection.
• Pressure reduction cools down the sample.
• Cold spots GASIFIER
• Retention outside the GC
• Sample discrimination
Sample Introduction Devices
Liquefied gas (LPG)
• Pressure
• Temperature Sample
treatment

Inject as Gas or as Liquid?

1% gas in sample volume is

Liquid 0.004% of composition

1% liquid in sample volume is

Gas 250% of composition

Preferably as a Liquid !
Sample Introduction Devices
Liquefied gas (LPG)
• Pressure
• Temperature Sample
treatment
SAMPLE
Inject as a Liquid BUMB

How ?

SAMPLE
IN
TESCOM
REGULATOR
PR
Carrier
HIGH GAS Gas
PRESSURE IN

SAMPLE OUT
TO VENT
RESTRICTION

Pressure station
Sample Introduction Devices

Use fully filled bombs

Else sample discrimination

Propane and Butane Mixture in a 1 liter bottle

100 ml gas
500 ml
gas
800 ml
gas
C3=50.0
C4=50.0 C3=49.9
C4=50.1 C3=49.3
C4=50.7 C3=47.0
C4=53.0
What about Valve Timing?
•Valve timing is either set at the factory if it is SP1 solution or
setup in the field typically by an Agilent engineer. SP1’s have
detailed manuals for setting up valve timing.

•Valve timing should not require adjustment and original settings

should be recorded and kept with the instrument at all times.

•If new columns are purchased they either need to be

preconditioned or conditioned on site prior to being set up within
the instrument (typically 20C below max temperature for at least
4 hours).
Natural Gas Analyzer (SP1 7890-0042)

Prior to Injection
Natural Gas Analyzer (SP1 7890-0042)
Injection
Natural Gas Analyzer (SP1 7890-0042)
Elution of Hydrocarbons
Natural Gas Analyzer (SP1 7890-0042)
Elution of Permanent Gasses
Typical NGA Chromatogram (SP1 7890-0042)
Configuration:
• 3-valve/4-column (packed column)/TCD
Sample type:
• Natural gas and similar gaseous mixtures

Page 67
Natural Gas Analyzer (SP1 7890-0192)
Configuration:
• 3-valve/4-column (packed column)/TCD
Sample type:
• Natural gas and similar gaseous mixtures
SP2 Wasson Tiger Program
Operation Conditions and Catalyst Check

Typical operation temperature is 400°C with 20mL/min of H2

being added post column, pre catalyst

You can check Catalyst functionality by having a standard with

known amounts of CH4, CO and CO2

Typically conversion efficiency is >70% so peak areas for the

same concentration of CH4, CO and CO2 should be around the
same size
Linearity of Methanizer
•DL is approx. 200 ppb using a 0.5 mL sample loop and
linear to approx. 10%.

•Large loops (up to 2mL) will result in a lower DL limit but

also a lower max. concentration.

•TCD and Methanizer / FID may be used in combination to

detect sub ppm levels of these gases as well as high %
levels.
Catalyst Poisoning and Practical Tips

•Very small amounts of H2S, SF6 and most other sulfur gases
cause immediate and complete deactivation of the catalyst,
Regeneration is not possible.

•It is uncertain as to whether large concentrations of O2 can

have a negative impact on the catalyst. For this reason it is
best to avoid sending large concentrations of O2 to the catalyst.
Catalyst Poisoning and Practical Tips

•Unsaturated hydrocarbons such as pure ethylene cause

immediate, but partial, degradation of the catalyst as evidenced
by slight tailing of CO and CO2 peaks.

•Any catalyst that is suspected of being poisoned should be

replaced and no attempt made to regenerate the material.
Questions?

October 29, 2014

74
 SUPELCO

Capillary GC Troubleshooting:
A Practical Approach

Katherine Stenerson
Gas Separations R&D
Supelco, Supelco Park, Bellefonte, PA 16823
 Outline

❚ Basic Troubleshooting Strategy

❚ Preventing Problems
❚ Identifying Common Problems
❚ Recommended Reading
❚ Discussion

©1999 Sigma-Aldrich Co. SUPELCO

 Troubleshooting Strategy

❚ Have appropriate equipment and

supplies on hand.
❚ Establish a systematic approach.
❚ Know what to look for first.
❚ Record what you did to correct the
problem.

©1999 Sigma-Aldrich Co. SUPELCO

 Suggested Equipment to Have on
Hand for Troubleshooting:

Electronic Leak Detector

Flow Meter
“Test” Column
Replacement Accessories (Syringes, Ferrules, Septa)
Replacement Purifiers

©1999 Sigma-Aldrich Co. SUPELCO

 Five Major Sources of
Chromatographic Problems:

❶Operator Error
❷The Sample
❸The Column
❹The GC Electrical System
❺The Gas Flow System (both internal and
external to the GC)

©1999 Sigma-Aldrich Co. SUPELCO

 Approaching the Problem

❚ Check first to see if a “fix” for the

problem is already known.
❚ Check the Supelco Capillary GC
Troubleshooting Guide (Bulletin 853.)
❚ Check back in the instrument
maintenance record.
❚ Talk to others in your lab.

©1999 Sigma-Aldrich Co. SUPELCO

 Isolate the Source of the Problem
OK Not OK
Check operating Correct the
Run Ref. Std.
parameters parameter
Not OK
OK

Problem was Install

sample Test
related Column

Not OK
OK Problem is in the Inlet
or with the carrier gas
OK
Problem
Cap off
was
Detector
Column related Problem is in the
Not OK
Detector

©1999 Sigma-Aldrich Co. SUPELCO

 When reviewing operating method
parameters consider the following:

? Is my starting temp. low enough to allow

sufficient sample focusing?
? For splitless injections, is my splitter opening
at the appropriate time?
? Is my column flow set to give me maximum
efficiency at the most critical point?
? Are heated zones (injectors, detectors,
interfaces) set appropriately?

©1999 Sigma-Aldrich Co. SUPELCO

 The Best Way to Solve Problems
is to Prevent Them!

❚ Install and maintain proper purification

for all gases in the GC system.
❚ Maintain the injector by periodically
inspecting and changing the liner,
septa, and seal (H/P™.)
❚ Use the proper injection technique-this
includes using the right liner for the job.
❚ When necessary, use a guard column to
protect the analytical column.

©1999 Sigma-Aldrich Co. SUPELCO

 Gas Purification

❚ Carrier Gas
❙ At minimum, remove hydrocarbons, water, and oxygen.
❚ Hydrogen (FID)
❙ At minimum, remove hydrocarbons.
❚ Air (FID)
❙ At minimum, remove water and hydrocarbons.
❚ Nitrogen make-up (FID, ECD)
❙ At minimum, remove hydrocarbons.
❚ P-5 make-up (ECD)
❙ At minimum remove hydrocarbons (especially halogen-
containing), oxygen.

©1999 Sigma-Aldrich Co. SUPELCO

 Acceptable Purity Levels for
Chromatography Grade Gases

Impurity / Maximum Concentration

Total
Gas O2 H2O CO2 CO Hydrocarbons
Helium <1.0 ppm <1.0 ppm <1.0 ppm <1.0 ppm <1.0 ppm
Nitrogen <1.0 ppm <1.0 ppm <1.0 ppm <1.0 ppm <1.0 ppm
Air 20-22% <1.0 ppm <1.0 ppm <1.0 ppm <1.0 ppm
Hydrogen <1.0 ppm <1.0 ppm <1.0 ppm <1.0 ppm <1.0 ppm
Argon/
Methane <1.0 ppm <1.0 ppm <1.0 ppm <1.0 ppm <1.0 ppm

©1999 Sigma-Aldrich Co. SUPELCO

 Suggested purifiers
Hydrocarbons Water Oxygen

Carrier Supelcarb HC Mole Sieve 5A OMI -2

Supelpure HC
H2

Air Mole Sieve 5A

N2 makeup

P-5 OMI -2 OMI -2

P-5

©1999 Sigma-Aldrich Co. SUPELCO

 What are some signs that my
purifiers need to be changed?

Hydrocarbon Traps Molecular Sieve 5A

Noise in the baseline (FID) Increase in column bleed
Increase in background Water visible in MS
peaks on tune (MSD) background
Higher than normal Poor peak shapes for
baseline reading on FID gaseous VOCs (purge and
trap)
Extra peaks visible in run
Extra peaks visible in run
OMI™-2 color change

©1999 Sigma-Aldrich Co. SUPELCO

 Injector Maintenance

❚ Change (as needed):

1. Liner and O-ring*
2. Seal and washer *
*H/P™ GCs

❚ Inspect the inlet periodically

-Look for contamination in the liner
-Look for residue on the seal

©1999 Sigma-Aldrich Co. SUPELCO

 Using the right liner and injection
technique can also prevent problems:

❚ Split Injection
❙ used for concentrated samples
❙ high flow of carrier gas through liner
during injection
❙ should use liner designed for split injection
❚ Splitless Injection
❙ used for trace analysis
❙ low flow of carrier gas through liner during
injection
❙ inertness and internal volume of liner used
are critical
©1999 Sigma-Aldrich Co. SUPELCO
 Some liners used for split
injection:
Cup (unpacked)

Cup (wool packed)

Split/splitless- wool packed

©1999 Sigma-Aldrich Co. SUPELCO

 Some liners used for splitless
injection

2 mm ID, straight

Dual-tapered

Single-tapered

©1999 Sigma-Aldrich Co. SUPELCO

 If you must clean a liner….

❚ Handle liners with gloves or forceps.

❚ Use clean compressed gas and/or a fine
brush to remove particles.
❚ Rinse liner in an appropriate solvent
and dry with clean compressed gas.
❚ Use mineral acid and/or detergent only
if absolutely necessary.

©1999 Sigma-Aldrich Co. SUPELCO

 Using a Guard Column

❚ Choose a guard column which has been

deactivated.
❚ Usually, the ID of the guard matches
the analytical column.
❚ A 5-10 meter length is normally used.
❚ Connect with either a GlasSeal™ or butt
connector.

©1999 Sigma-Aldrich Co. SUPELCO

 Common Problems

1 Poor Peak Shapes (either tailing,

fronting, or just generally ugly.)
2 Nonlinearity
3 Baseline Noise and /or Drift
4 Ghost Peaks
5 Missing Peaks / Poor Response
6 Insufficient Resolution
©1999 Sigma-Aldrich Co. SUPELCO
 1. Poor Peak Shapes

❚ Fronting can indicate

column overload.

||

||

❚ Tailing can indicate

activity in the system
or improper column
installation.
©1999 Sigma-Aldrich Co. SUPELCO
 1. Poor Peak Shapes (cont.)

❚ Generally ugly peaks, such

as a,a-
dimethylphenethylamine,
can be caused by a variety
of problems.

©1999 Sigma-Aldrich Co. SUPELCO

 2. Nonlinearity

The most common causes are:

➨Column overload
➨Detector overload
➨Standards preparation
➨Poor peak shape resulting in improper
integration

©1999 Sigma-Aldrich Co. SUPELCO

 An Example of Overload:

Peaks have broad bases,

fronting on last few visible in
run.

©1999 Sigma-Aldrich Co. SUPELCO

 Preventing column overload for
splitless injections:

❚ Inject a smaller amount / use a 1 ul

syringe.
❚ Use a thicker film column.
❚ Use a column with a wider ID.
❚ Decrease upper limit of calibration
range.
❚ Use a column of slightly different
polarity.
©1999 Sigma-Aldrich Co. SUPELCO
 An example of poor peak shape
affecting linearity:

❚ Benzoic acid is
typically of poor
shape when doing
splitless injections.

©1999 Sigma-Aldrich Co. SUPELCO

 3. Common causes of baseline
noise / drift.

❚ Column bleed
❚ Dirty detector
❚ Contaminants in carrier gas / carrier
gas purity

©1999 Sigma-Aldrich Co. SUPELCO

 Effect of carrier gas purity on baseline
noise:
12000
11500
11000
10500
10000
9500
9000
8500
8000
7500 H2 carrier from tank
7000
6500
6000
5500
5000
4500
4000
3500
3000
2500
2000
1500
1000
500
0
H2 carrier from a generator
1

©1999 Sigma-Aldrich Co. SUPELCO

 Column bleed results from the
normal degradation of the
stationary phase.

❚ All columns bleed to some extent.

❚ Bleed increases with temperature.
❚ The amount of bleed will increase in the
presence of oxygen.

©1999 Sigma-Aldrich Co. SUPELCO

 A Typical Bleed Profile:

Bleed measured as the

difference between 1 and 2.

©1999 Sigma-Aldrich Co. SUPELCO

 Column Bleed on an MSD

❚ Visible as baseline rise in the TIC.

❚ Check spectra for key bleed ions:
❙ PTE™-5: 207, 281
❙ SPB™-1: 73, 207, 281
❙ SPB™-624: 207, 269
❚ Make sure interface temp. is < column
max. temp.

©1999 Sigma-Aldrich Co. SUPELCO

 Ion 207 corresponds to a fragment known as D3:

CH 3 CH 3

Si
O O
+
Si Si
CH 3 O CH 3

CH 3

©1999 Sigma-Aldrich Co. SUPELCO

 MS spectra of bleed from a PTE™-5 Column
Abundance

Scan 2895 (27.487 min): 1118015.D

207
6000

5500
207
5000

4500

4000

3500

3000

2500

281
2000

1500
73 281
96 133

1000 191
253

500 50

115 162 223 327 355

415
0
40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400
m/z-->

©1999 Sigma-Aldrich Co. SUPELCO

 MS spectra of bleed from an SPB™-1 Column

Abundance

Scan 1941 (28.793 min): 0122002.D

11500 73
11000

10500

10000

9500

9000 73
8500

8000

7500

7000

6500
44
6000
207
5500

5000

4500

4000

3500
207 281
3000

2500 147

2000
281
341
1500

1000
96 119 179
500 253 429
313 401
0
40 60 80 100120140160180200220240260280300320340360380400420
m/z-->

©1999 Sigma-Aldrich Co. SUPELCO

 MS spectra of bleed from an SPB™-624 Column
Abundance

Scan 8581 (33.704 min): 1022006.D

24000 207

22000

20000 207
18000

16000

14000
269
12000

269
10000

8000

6000 44
253
4000 133 191
73 96
147 177
2000 283
119 322 343
59 163 223239
298
0
40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340
m/z-->

©1999 Sigma-Aldrich Co. SUPELCO

 MS Spectra of Septa Bleed
Abundance

Scan 604 (7.460 min): 1201001.D

44000 73

42000

40000

38000

36000
73
34000

32000

30000

28000

26000 147
24000

22000

20000
147
281
18000

16000
281
14000

12000

10000

8000

6000
327
45
4000
207
2000 399415
131 191 251 343 383
95 115 163 223 297
0
40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420
m/z-->

©1999 Sigma-Aldrich Co. SUPELCO

 Prevent column bleed!

❚ Sufficiently purge column with carrier before

ramping it up in temperature.
❚ Make sure carrier gas is filtered for water and
oxygen.
❚ Check integrity of all fittings leading to the
column.
❚ Do not heat the column above its maximum
temp.
❚ Precondition the column prior to use.
©1999 Sigma-Aldrich Co. SUPELCO
 4. Ghost Peaks

❚ Residue in the inlet liner and at the

head of the column
❚ Contaminated syringe / and or wash
solutions on an autosampler.
❚ Sample carryover
❚ Contaminated carrier gas

©1999 Sigma-Aldrich Co. SUPELCO

 If pieces of septa get into an inlet liner...

2200000

2000000

1800000

1600000
Response test mix, before
1400000

1200000

1000000

800000

600000

400000

200000

©1999 Sigma-Aldrich Co. SUPELCO

 …even a simple analysis can be ruined.

3500000

3000000

2500000
Response test mix, after
2000000

1500000

1000000

500000

Time-->

©1999 Sigma-Aldrich Co. SUPELCO

 5. Missing Peaks / Poor
Response
❚ Sample decomposition
❙ Activity in the inlet or column
❙ Injection port temperature too high
❙ Sample not stable enough for GC
❙ Standards not stable
❚ Coelution
❚ Insufficient run time / final temperature
❚ Sample not volatile enough for GC
❚ Improper column installation
©1999 Sigma-Aldrich Co. SUPELCO
 Nasty samples can damage a column
by creating active sites:

450000 Before Sample Injection

400000

2-methyl-3,5-dinitrophenol

pentachlorophenol
350000
2,4-dinitrophenol
300000 4-nitrophenol

250000

200000

150000

100000

50000

©1999 Sigma-Aldrich Co. SUPELCO

 Here, the responses of some acids
were affected:
Abundance

After sample injection

2,4-DNP & 4-NP should be here

900000

Pentachlorophenol should be here

800000

2-methyl-3,5-dinitrophenol
700000

600000

500000

400000

300000

200000

100000

Time-->

©1999 Sigma-Aldrich Co. SUPELCO

 Response can also be affected by the
position of the column in the inlet:

2800000
2600000

2400000

2200000

2000000
8 mm above top of ferrule
1800000

1600000

1400000

1200000

1000000

800000

600000
400000

200000

©1999 Sigma-Aldrich Co. SUPELCO

 Here, the column was not inserted far
enough:

2200000
2000000

1800000

1600000 5 mm above top of ferrule

1400000

1200000

1000000

800000

600000

400000

200000
0

©1999 Sigma-Aldrich Co. SUPELCO

 Here, the column was inserted too far:

1800000
1600000

1400000

1200000
20 mm above top of ferrule
1000000

800000

600000

400000

200000

©1999 Sigma-Aldrich Co. SUPELCO

 6. Insufficient Resolution

❚ Wrong column
❙ Longer columns increase resolution.
❙ Smaller ID columns increase resolution.
❙ A different phase altogether may be
needed.
❚ Wrong Conditions
❙ Carrier gas flow too fast or slow .
❙ Oven ramp rate too fast.

©1999 Sigma-Aldrich Co. SUPELCO

 Recommended Reading
Supelco Bulletins
1. 741: The Supelco Guide to Leak-Free Connections
2. 783: Cleaning Flame Ionization Detectors
3. 853: Capillary Troubleshooting Guide
4. 875: Supelco Capillary GC Selection Guide
5. 895: Installation and Maintenance Instructions for
.25 mm and .32 mm ID Fused Silica Capillary
Columns
6. 897: Installation and Maintenance Instructions for
.53 mm ID Fused Silica Capillary Columns
7. 898: Gas Management Systems for GC
8. 899: Capillary GC Inlet Sleeve Selection Guide
9. 916: Purge and Trap System Guide
10. 918: Selecting Purifiers for Gas Chromatography
©1999 Sigma-Aldrich Co. SUPELCO
 Help is just a phone call or
mouse click away!

❚ Supelco Technical Service

phone: 1-800-359-3041
email: [email protected]
❚ Supelco Customer Service
phone: 1-800-247-6628
email: [email protected]
❚ Sigma-Aldrich Website
www.sigma-aldrich.com
©1999 Sigma-Aldrich Co. SUPELCO
 GC
Troubleshooting

BUILD A CULTURE OF LEARNING WITH

CRAWFORD SCIENTIFIC | CHROMACADEMY
 TABLE OF
CONTENTS
P.03
5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM
A picture paints a thousand words. The art of GC troubleshooting often lies in being able to recognize a problem
from the evidence presented in the chromatogram or baseline appearance.

P.13
GC COLUMN MAINTENANCE - PREVENTION IS BETTER THAN CURE
Using proper procedures for capillary GC column storage and conditioning can have a major impact on column
lifetime and the quality of results obtained.

P.22
10 COMMON GC MISTAKES
10 things to watch out for!

P.28
SOLVENT CHOICE FOR GC INJECTION – A CRITICAL METHOD VARIABLE!
I guess we all have our ‘go to’ solvents for our work in GC, and most of the time this will be based on the availability
of the solvent and the chemical nature of our samples.

P.33
GC INLET MAINTENANCE... HAVE YOU REALLY HEARD IT ALL BEFORE?
Many troubleshooting investigations in chromatography often don’t lead to a single causal factor. Often, the reason
for problems or lack of method robustness are related to many small ‘contributory factors’ and this is particularly
true of the problems associated with sample introduction in capillary Gas Chromatography.

GC Troubleshooting E-book Page 2

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR
GC ANALYSIS – AND HOW TO FIX THEM

1) Irreproducible Retention Times

pH meters are calibrated to give the correct pH readback in aqueous solution – the buffers you verify this with are aqueous.
If you measure the pH with the organic added, the pH will be different to that of measuring before organic addition.
However, the most important point is to be consistent. If you do always measure pH after the organic is added, make
sure you state this in the method so that everyone does it the same way. It won’t be 100% accurate, but at least it will be
consistent. This is probably more important than having the exact pH.

There are two types of retention time variability that can be observed. Firstly, from injection to injection, this could be from
injection to injection in a run of samples or multiple injections from the same vial. This may be caused by changes in carrier
gas linear velocity due to a defective electronic flow controller, leaking septum or column connection, or variable gas supply
due to a leak in the gas supply tubing. Under these circumstances you would expect to see variable retention times for all
analytes.

To remedy the problem ensure that the instrument settings are correct and occasionally verify that the instrument
calculated flow/linear velocity matches the carrier gas flow by measuring all inlet flows using a flow meter.

Other causes of this type of variable retention time are variations in the oven temperature (either from a faulty temperature
controller or from insufficient thermal equilibration time) or if the inlet pressure is not high enough to sustain flow at high
gradient temperatures. In constant flow operating mode, the carrier pressure is ramped to attain a constant flow through
the temperature program (as the temperature is increased carrier gas viscosity also increases, and therefore, requires a
higher pressure to maintain constant flow), in constant pressure mode the inlet pressure remains constant which means

GC Troubleshooting E-book Page 3

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM

that as the carrier gas viscosity increases during the temperature program the linear velocity will decrease causing retention
times to change. With mass-flow or flow sensitive detectors, this phenomenon can also manifest itself as either a gradually
increasing or decreasing baseline signal depending upon the response characteristics of the detector.

Therefore, it is often better to use constant flow mode to avoid these problems. Figure 1 demonstrates the improvement in
chromatography when using constant flow mode; there has been an overall gain in sensitivity (peak areas have increased)
mainly due to the decrease in peak width, the rising baseline has been eliminated due to the constant flow into the mass-
flow sensitive detector which allows for more reproducible integration and quantitation, and finally retention time has
decreases by a factor of three.

Figure 1: Constant flow vs. constant pressure analysis.

GC Troubleshooting E-book Page 4

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM

If you have long term variability in retention times, this may be attributed to changes in the column, such as, stationary
phase degradation or shortened column due to trimming which when entered incorrectly into the GC data system causes
the instrument to incorrectly calculate the linear velocity of the carrier gas. Remember, the EPC calculates all flows from the
applied pressure, the nature of the carrier gas, and the column dimensions.

However, how important is it to know the exact length of the column? Columns are regularly cut by users, with varying
unspecified lengths being removed. It would be impractical to expect users to record the exact length of the small pieces of
column that are generally removed and it is totally impractical to measure the length of the existing column - the standard
length being 30 m. Having to unwind and rewind 30 m would likely damage the column. In general removal of these small
portions has negligible effect on the performance of the column (e.g. removal of a typical length of 3 cm from a 30 m column
equates to 0.1% of total length).

The assessment of exact column length is of no benefit whatsoever for the majority of applications and is better served
by applying meaningful system suitability criteria to critical parameters within the method that are affected by reducing
the column length - this would be absolute retention time, resolution, and possibly some effect on peak area due to slight
changes in the split ratio. The criticality of these parameters has to be assessed on a method by method basis and adequate
provisions made for system suitability criteria that are relevant, meaningful, and have sensible limits applied. In general
these would be tests such as retention time limits, resolution limits, and linearity.

There are certain cases where reduction in column length is more significant - either with short columns (10 m or less) or
columns which are exposed to excessive contamination and need larger lengths removed more regularly. This should be
captured by system suitability or by use of retention gaps. If the column is too short, retention times will be too short and
vice versa.

GC Troubleshooting E-book Page 5

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM

2) Integration Issues

In this case it is difficult to reliably integrate the peaks as there is a rising baseline. The first solution to avoid this problem
would be to eliminate any type of baseline drift in the first place. This can be done by reducing column bleed by properly
conditioning the column, using constant flow or linear velocity mode especially when using a temperature program, or if you
need to use constant pressure mode and are using a mass-flow sensitive ionizing detector you may have the ability to use
variable make-up flow to compensate for the change in linear velocity during the method.

A great tip to help condition the column correctly and in the most efficient manner is, once the column has been connected
to the inlet do not connect it to the detector and allow at least six column volumes of carrier gas to pass through the column
in order to remove air from the column as well as sparging any dissolved oxygen from within the stationary phase (Table 1).
This will allow you to condition the column for less time and at a lower temperature. Once this step has been completed,
ramp the oven temperature (ensure the carrier gas is still flowing through the column) at 20 °C/min. to 20 °C above the
upper temperature required by the analytical method. Once the upper temperature limit has been reached the column
should be conditioned for the correct amount of time based on the dimensions and phase type (Table 2).

Column Internal Minimum Flow Minimum Purge

Diameter (mm) Rate (mL/min.) Time (min.)

0.53 5 10

0.32 1.5 20

0.25 1 25

0.18 0.8 30

0.1 0.5 40

Table 1: GC column purge times.

GC Troubleshooting E-book Page 6

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM

Phase Type Length (m) Film Thickness Conditioning Time

(mm) (min.)
Non-polar < 30 <0.5 15
0.5-1.0 30
>1.0 60
30-60 <0.5 30
0.5-1.0 45
>1.0 60
>60 <0.5 60
0.5-1.0 90
>1.0 120
Mid-polarity < 30 <0.5 20
0.5-1.0 40
>1.0 60
30-60 <0.5 40
0.5-1.0 60
>1.0 80
>60 <0.5 80
0.5-1.0 120
>1.0 160
Polar < 30 <0.5 30
0.5-1.0 45
>1.0 60
30-60 <0.5 60
0.5-1.0 90
>1.0 120
>60 <0.5 80
0.5-1.0 120
>1.0 160

Table 2: Recommended conditioning times for various capillary GC column types.

It is always good policy to record the bleed profile for a column when new (Figure 2), so that the level of bleed can be
referenced at a later date in order to assess the degradation of the stationary phase over time, and perhaps a performance
limit established for column replacement.

Simply run the method without making an injection or inject a small amount of sample solvent. If you are using mass
spectral detectors, the presence of ions at m/z 207, 281, and 355 indicate column bleed.

These will almost always be there – it is whether they are causing problems either spectrally or in terms of reproducibility of
integration that really matters.

GC Troubleshooting E-book Page 7

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM

Figure 2: Typical capillary GC stationary phase bleed profile for two different polysiloxane based stationary phases.

Another approach to avoiding column bleed is to consider the stationary phase and column type you are using. High
polarity columns inherently bleed more; therefore, using the lowest polarity column possible can help to avoid some
unwanted bleed. You can also consider using a GC-MS designated column (even if you are running a GC method) as they
have been designed to be low bleed. They will provide better sensitivity due to the improved signal to noise ratio and will
give better mass spectral purity from the absence of background bleed ions (Figure 3).

Figure 3: Comparison of 35% phenyl standard GC and GC-MS designated column.

GC Troubleshooting E-book Page 8

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM

In the real world rising baselines are often inevitable, therefore, spending some time familiarizing yourself with the advanced
integration settings in your data system will allow you to properly integrate challenging chromatograms - these settings
include threshold, slope sensitivity, baseline reset points, and different integration methods, such as, valley-to-valley.
Remember to always use the same integration method every time to provide consistent results (Figure 4 and 5).

Figure 4: Common peak integration errors.

Figure 5: Peak integration methods. 1) Drop perpendicular, 2) valley to valley, 3) tangential skim, 4) exponential skim,
5) Gaussian skim

GC Troubleshooting E-book Page 9

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM

3) Step-Shaped Peaks

The step-shape can either be before or after the peak, and may also be accompanied by tailing or a shoulder, and is due
to analyte thermal degradation in the inlet. To remedy this problem reduce the inlet temperature in 20 °C steps until a
normal peak shape is achieved. However, take care not to lower the inlet to a temperature that is too low to achieve proper
volatilization of all of your analytes, if this happens you may begin to see irreproducible peak areas.
To choose an appropriate inlet temperature the following steps can be followed:

• A good starting point for method development and for new analyte applications is 250 °C
• A scouting temperature program can be used to estimate the elution temperature of the highest boiling component
(Figure 6). Set the inlet temperature at least 50 °C above this temperature to ensure sufficient sample volatilization

Figure 6: Scouting temperature program.

GC Troubleshooting E-book Page 10

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM

4) Poor Peak Shape (Early Eluting Peaks)

Poor peak shape for early eluting analytes when you are carrying out a
splitless injection is caused by a sample solvent/column polarity mismatch
or the wrong initial oven temperature (the oven temperature is too high). In
splitless injection the sample transfer from the liner to the column is slow;
therefore, to mitigate band broadening effects from this the sample must be
refocused at the head of the column. Two focusing mechanisms occur (Figure 7):

1. Solvent focusing, where low boiling analytes remain dissolved in the solvent which condenses on the inner wall of the GC
column at low initial oven temperatures. The solvent polarity must match that of the column to ensure a contiguous film
is deposited leaving a narrow sample band when the solvent evaporates
2. Cold trapping, where higher boiling analytes are condensed in a tight band in the temperature gradient between the inlet
and the column oven. Initial oven temperatures should be set 20 °C lower than the boiling point of the solvent used to
dissolve the sample

Figure 7: Splitless injection focusing mechanisms.

GC Troubleshooting E-book Page 11

5 PICTURES WHICH REVEAL PROBLEMS WITH YOUR GC ANALYSIS – AND HOW TO FIX THEM

5) Loss of Resolution From Loss of Efficiency

In order to diagnose this problem carry out a plate count (your software will
probably do this) on the peaks. If you are seeing a loss in efficiency the plate count
will reduce, in particular for early eluting peaks (Figure 8).

There are several causes of this problem including, poor column cut and installation
which leads to analytes being held up at the entrance to the column resulting in a
broadened peak, loss or contamination of the stationary phase (this can be resolved
by trimming the column), or the incorrect column length or diameter entered into
the data system which results in an incorrect carrier gas velocity which in turn affects
efficiency (remember each carrier gas has an optimum linear velocity to produce
chromatography with the best efficiency).

Internal Film Column Theoretical Theoretical

Diameter Thickness Length (m) Plates Plates per
(mm) (μm) Meter N/m*

0.18 0.18 20 133200 6660

0.25 0.25 30 138900 4630

0.32 0.32 30 112800 3760

Table 3: Typical column efficiencies. *Measured with a k = 5.

Figure 8: Plate count.

Where:
tr = retention time
Wb = peak width at base
W1/2 = peak width at half height

GC Troubleshooting E-book Page 12

GC COLUMN MAINTENANCE
PREVENTION IS BETTER THAN CURE

Using proper procedures for capillary GC column storage and conditioning can have a major impact on column lifetime and
the quality of results obtained. This ‘Tips and Tricks’ instalment covers everything you wanted to know but were never told
about proper GC column maintenance.

Column Storage
Correct column storage is necessary to prevent two major occurrences – the ingress of atmospheric oxygen and moisture
into the column and the oxidative degradation of the bonded stationary phase through UV catalyzed mechanisms. The
following guidelines will help ensure longer column lifetime:

• Remember to seal the column ends when they are not in use to exclude atmospheric oxygen and moisture. The easiest
way is to seal the column using silicone septa (cut them in half – it’s less expensive!!) or column sealing caps.
• Don’t leave the column out on the bench where it can be damaged. Store the column so it will not be scratched. If
scratched, the stress to the column may cause it to crack during operation.
• Store the column boxed with the test chromatogram in a dark place. Exposure to high levels of ultra-violet light can
initiate oxidization of the stationary phase.

If the column is to remain on the instrument a constant low flow of carrier gas should be maintained with the split flow on.
If the split flow is switched off back diffusion of air into the column can occur; this air can then cause damage. In order to
prevent a build-up of moisture and air in the oven it should be left on at a
temperature of 60 °C.

Oxygen rapidly degrades the stationary phase by cleaving bonds along the back-bone of the column. This is known as a
“cyclic backbiting reaction” where the siloxane chain breaks into more thermodynamically stable, but also more volatile,
cyclic siloxanes (Figure 1). It is the elution and detection of these cyclic siloxanes which constitutes column bleed. This
damage is irreversible. The cyclic structures which are formed during this process have characteristic mass spectra at m/z
207, 281, and 355.

GC Troubleshooting E-book Page 13

GC COLUMN MAINTENANCE - PREVENTION IS BETTER THAN CURE

Figure 1: Typical capillary GC column bonded phase ‘backbiting’ bleed reaction.

The increase in the number of Si-OH groups within the oxidized phase will lead to an increase in the number of secondary
silanol (Si-OH) interactions and peak tailing may be observed (Figure 2). This effect is most noticeable with polar and basic
compounds.

Figure 2: Peak tailing of polar compounds due to secondary interactions with exposed silanol groups in a column
showing bleed symptoms.

GC Troubleshooting E-book Page 14

GC COLUMN MAINTENANCE - PREVENTION IS BETTER THAN CURE

Column Bleed
Column bleed happens with all columns, all the time. It is the continuous elution of compounds produced from the degra-
dation of the stationary phase as described above (Figure 1). It is important to ensure that the amount of column bleed is
minimal and constant, i.e. a flat baseline is achievable at low detector response.

In general, polar stationary phases and thicker films bleed to a greater extent. Bleed is normally seen as an increase in signal
at increasingly higher temperatures when operating the GC in constant flow mode and when conditioning a newly installed
column (Figure 3). Bleed may appear to be worse when using detectors that are particularly sensitive to the cyclic siloxane
bleed products. Examples are; cyanopropyl phases with NPD detection and polyethylene glycol phases with electron capture
detectors.

Bleed is best measured as the difference or change in signal at two temperatures, usually around 100°C and at the column’s
upper isothermal temperature limit. Of course, the signal at both temperatures will have a contribution from background
generated from system components that must be subtracted to determine bleed values accurately.

Figure 3: Measurement of relative column bleed.

Excessive column bleed appears as a larger rise in the baseline at the higher temperature regions. There is no absolute
measurement to indicate when column bleed is excessive.

Column bleed is best measured as the difference or change in the background signal at two temperatures - Relative Bleed.

Usually the column’s upper temperature limit and a lower value around 100oC are used. The absolute background signal is a
composite of the background generated by the entire GC system. It is not possible to determine the contribution of column
bleed to this total background signal. By measuring the relative amount of column bleed, the other contributors to the back-
ground signal are subtracted out.

Most columns are tested using FIDs - the output signal for which is measured is in picoamps (pA). Bleed levels are usually
reported as the difference (DpA) in the FID signal at two temperatures (4.3 or 8.6 DpA in the example shown here).

GC Troubleshooting E-book Page 15

GC COLUMN MAINTENANCE - PREVENTION IS BETTER THAN CURE

Figure 4: Excessive column bleed.

The bleed profile should be continuous, with no discrete peaks and should begin at around 30-40 °C below the column
upper temperature limit, with the profile flattening to a constant signal level. The column will normally have two upper
temperature limit values – the lower temperature is the isothermal limit and the column may be operated at this
temperature indefinitely without significant degradation of column performance (Figure 5).

The upper temperature limit of the column is the gradient limit and this temperature may be maintained for 10-15 minutes
before significant degradation of the column performance. The upper temperature limits of the column should not be
exceeded. Column bleed will increase with column use, exposure to oxygen (usually due to poor conditioning practice or
air leaks from loose fittings, compromised septa or exhausted gas traps), using the column at or near the upper gradient
temperature for prolonged periods, or through the repeated use of aggressive solvents such as tetrahydrofuran, water, or
acetonitrile.

Figure 5: GC column temperature limits.

Low bleed phases and ‘MS’ designated phases are now available from many manufacturers that show reduced bleed at
elevated temperatures and are especially useful for high sensitivity applications with Mass Spectrometric Detectors. Many
phases use an altered ‘phenylene’ chemistry with phenyl phases which have the functional moiety included in the polymeric
backbone rather than as a silicon substituent, resulting in reduced de-polymerization and oxidation of the phase (Figure 6).

Figure 6: ‘Phenylene’ type low bleed phase chemistry (left) and a ‘standard’ polysiloxane backbone (right).
Note - selectivity between traditional 5% phenylmethylpolysiloxane phases and the ‘phenylene’ equivalent may vary slightly.

GC Troubleshooting E-book Page 16

GC COLUMN MAINTENANCE - PREVENTION IS BETTER THAN CURE

It is important to regularly check the condition of self-indicating gas traps or calculate the usage of non-indicating traps (6
bottles of gas maximum prior to a trap change is recommended). It is important to protect the columns from both oxygen
and moisture using the correct gas trap. Column fittings should also be regularly tested for leaks using a highly sensitive
leak detector.

One major source of column contamination comes from the carrier stream just prior to the bottle running out of gas. Even
in gas bottles containing dip tubes there will be excess moisture and other dissolved components significantly above the gas
specification levels (typically 0.99999% purity) in the ‘dregs’ of the carrier. Most manufacturers (and bottled gas suppliers)
recommend that cylinders are changed when the bottle pressure (stage 1 of the two stage regulator) falls to about 10% of
the original fill value (about 200-250 psi on a ‘Size K’ cylinder).

Column Conditioning
The column should be conditioned at 20-30 °C above the final temperature of the gradient program or the isothermal
temperature in the intended method of use, but the upper gradient programming temperature limit of the column should
not be exceeded.

After installing the column purge with carrier at room temperature for around 10-15 minutes at the flow rate required by
the analytical method prior to raising the temperature – this ensures the removal of dissolved air within the stationary phase
preventing unnecessary oxidation. For most columns a conditioning time of around one hour is more than sufficient (even
for polar and thick film columns).

Once the signal plateaus (usually following a sharp increase and shallow decrease), at the conditioning temperature the
column may be considered as being conditioned, however for applications that require very high sensitivity (good signal to
noise performance), the column should be held at the conditioning temperature for up to three hours (Figure 7).

Figure 7: Typical chromatogram before and after column conditioning. Note the lower bleed at high temperatures and the
reduction in background noise throughout the chromatogram.

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GC COLUMN MAINTENANCE - PREVENTION IS BETTER THAN CURE

Phase Fouling and Contamination

Analyte, matrix components, and solvent impurities can all contaminate the column. The contaminants may either be
involatile, in which case they will be deposited onto the stationary phase, or semi-volatile, and will elute over extended
periods causing baseline disturbances. Involatile impurities will tend to accumulate at the head of the analytical column
giving rise to many chromatographic problems including, broad, tailing, and split peaks especially when using splitless
injection (Figure 8). Peak shape problems usually arise due to an interference with the gross separation and focusing
processes that occur at the head of the analytical column.

As fouling normally occurs at the head of the column it is possible to trim the column and, therefore, restore optimum
performance. Trimming up to 5% of the column length is normally adequate; however, if this does not improve any peak
shape problems then a further 5% can be trimmed. It has been postulated that trimming the column will affect resolution;
although it should be remembered that resolution is not directly proportional to column length and doubling column length
only provides a 1.4x improvement in resolution. Any concerns can be alleviated by revalidating with a known method.

Figure 8: Distorted peak shapes resulting from contaminated stationary phase

(disubstitued aromatic amines, 14% cyanopropylphenyl stationary phase).

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GC COLUMN MAINTENANCE - PREVENTION IS BETTER THAN CURE

Chemical Damage
Most GC columns will have good chemical resistance except towards inorganic acids and bases; H2SO4, HCl, NH3, KOH, NaOH,
H3PO4, HF etc. When a GC column has been exposed to these types of compounds it will exhibit column bleed, a lack of
inertness (evidenced by peak tailing), and a loss of retention and resolution.

The use of perfluoroacids, such as trifluoroacetic, pentafluoropropanoic and heptafluorbutyric acid can damage the
stationary phase, however, they have to be present in high levels, 1% or higher.

Cutting 0.5-1 m from the front of the column can remedy the effects of damage. To prolong the column lifetime a guard
column or retention gap can also be used, although these may also be damaged by harmful substances and trimming or
replacement will be necessary; this, however, is a lot more cost effective than replacing a GC column.

Peak Fronting caused by column overload

An old or highly oxidized column is likely to show symptoms of ‘overloading’ due to the loss of phase at the head of the
column resulting in lowered capacity and efficiency. Fronting peaks may be observed (Figure 9).

Figure 9: Peak fronting due to column overload ultimately caused by loss/occlusion of stationary phase.

Retention Gaps
Up to 5 meters of deactivated silica tubing known as a Retention Gap may be connected via a simple push-fit union to the
analytical column. Retention gaps are used to:

• Trap the non-volatile residues from samples that may potentially contaminate the analytical column. The retention gap
acts to retain the non-volatile materials but does not interact with the analyte species. Regular trimming of the column
inlet may take place to avoid peak shape problems caused by contaminant build up.

• Alleviate the problems associated with polarity mismatch, as well as some of the peak shape problems associated
with on-column and large volume injection. The deactivated uncoated retention gap material allows the formation
of contiguous films with most solvents that will tend to focus the analyte on the stationary phase at the head of the
analytical column. Solutes eluting closest to the solvent front or those that most closely match the polarity of the solvent
will show the greatest peak shape improvements when a retention gap is used.

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GC COLUMN MAINTENANCE - PREVENTION IS BETTER THAN CURE

Leak Checking
It is important to check for leaks to minimize the ingress of air and moisture which can damage the GC column. Regular leak
checking should be part of the routine maintenance schedule, especially after any new connections have been made (i.e.
changing the column, routine maintenance etc.). Leak detectors can be used or if a mass spectrometer is connected as the
detector the leak detection function can be employed. A leak will produce a distinctive mass spectrum with peaks at m/z 18,
28, 32, 44 or 14, 16 which correspond to H2O, N2, O2, CO2 or N, O. Usually if m/z 28 is larger than m/z 18 there is a leak.

Column Rinsing
A capillary GC column must have a bonded and cross-linked stationary phase to be compatible with solvent rinsing.
Solvent rinsing kits can be purchased from any column manufacturer (Figure 10). The process of rinsing involves passing
millilitres of solvent through the column.
An injection of a large volume of solvent will NOT have the same effect and contaminants will not be removed from the
column.

Before rinsing 50 cm should be cut from the inlet end of the column. The inlet end of the column is then inserted into the
vial of the rinse kit which is attached to a pressurized gas source (N2, He). Successive solvents are then passed through
the column by applying 10-15 psi of pressure from the pressurized gas source (a flow of 1 mL/min is desirable). If viscous
solvents are being used longer rinse times may be required. After the last solvent has been passed through the column
the pressurizing gas is allowed to flow for 5-10 minutes before the column is properly re-installed into the GC system and
conditioned as normal.
Solvents which are appropriate for column rinsing and will provide good results are methanol, dichloromethane, and hexane
which are applied in series. Other solvents will also work (and may be required depending on the samples which have been
analysed), however, the following criteria should be met:

• A polar and non-polar solvent should be used.

• The most polar solvent should be used first followed by the other solvents in order of decreasing polarity.
• Using the injection solvent is advisable as the sample components should be soluble in it.
• Each successive solvent should be miscible with its predecessor.
• Water followed by methanol should be used if aqueous-based samples have been analysed
(i.e. biological extracts, waste water, soil etc.).
• Halogenated solvents should be avoided as the final rinse solvents if the detector installed is an electron capture detector
(ECD). Acetonitrile should not be used if a nitrogen phosphorous detector (NPD) is installed.

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Suggested solvent volumes for different column diameters are detailed in Table 1.

Column I.D. (mm) Solvent Volume (mL)

0.18-0.2 3-4

0.25 4-5

0.32 6-7

0.45 7-8

0.53 10-12

Table 1: Solvent volumes for rinsing columns.

Using larger volumes will not damage the column.

Figure 10: GC column rinsing kit.

Extending GC column lifetime

Once the GC column has been correctly fitted it is desirable to achieve the best possible results for as long as possible, so
here are some final tips for extending column lifetime.

1. Fit carrier gas traps close to the instrument (to remove oxygen and moisture) this is a great way to improve column
lifetime and detection limits.
2. Use the plate count of a test analyte to monitor column efficiency and set a column discard limit based on your
knowledge of required plate counts for your types of analysis.
3. Columns can often be miraculously restored to life by trimming 5% of the total column length from the inlet end — note
that retention times may shift slightly after this operation, but efficiency may increase and peak shapes will improve.
Retention time changes can also be mitigated by using the instrument software to accurately calculate the length of the
cut column. This typically involves inputing the column dimensions, as denoted on the column ID tag, and the retention
time of an unretained peak - volatile gases such as propane or butane or volatile solvents such as methanol at higher
temperatures with an FID.
4. Consider using a guard column if your samples are particularly dirty.

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10 COMMON GC MISTAKES

1) Not Taking Enough Care at the Inlet

Any leak in GC will cause significant problems with chromatography and the inlet is the most likely area. Don’t take the risk
of having to troubleshoot a leak, change the septum regularly and make sure the column is correctly installed and leak-free.

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10 COMMON GC MISTAKES

2) Turning the oven on before the carrier gas

If there’s one thing that will permanently damage a column more quickly than anything else it’s heating the column without
any carrier gas flowing. Get into the habit of making sure the carrier gas is flowing before you switch on the oven AND make
sure the oven is cool before switching the carrier off. When switching the oven off, set the oven temperature to 35oC before
switching the oven off as this will cool much quicker.

3) Not programming in column dimensions

Most modern GCs use an EPC (electronic pneumatic controller) to accurately deliver carrier flows and this relies totally on
the correct column dimensions being entered by the operator. Make sure anytime you change the column you enter the
correct dimensions into the GC or else your flowrate and split ratios will be wildly inaccurate.

4) Not using optimal flowrate for carrier

Each carrier gas has an optimal linear velocity, which gives the best efficiency (Nitrogen c.12cm/sec, Helium c.35cm/sec and
Hydrogen 40 - 50cm/sec).

To obtain this optimal linear velocity the flowrate is matched to the internal diameter of the column in use. e.g. for a 0.32mm
ID column using helium the optimal flowrate will be about 2.0ml/min.

If the optimal flowrate is not used, column efficiency can be significantly reduced.

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10 COMMON GC MISTAKES

5) Using too large an injection volume

When a liquid sample is injected into the GC inlet, this vapourises into a much larger volume of gas. The size of the vapour is
dependant on the solvent being used and the injection volume.

If this volume exceeds the size of the liner a condition called backflash occurs.

Using a higher split ratio does not reduce this affect, you must either reduce the injection volume, use a different solvent or
use a larger liner.

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10 COMMON GC MISTAKES

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10 COMMON GC MISTAKES

6) Not specifying constant flow / constant pressure

As the oven temperature increases, the pressure within the column increases. In a constant pressure system, flowrate will
decrease to maintain a constant pressure. This increases retention time and decreases efficiency as the flow moves away
from the optimal linear velocity. In constant flow mode, the instrument maintains a constant flow (with optimal linear
velocity) by increasing pressure. Retention times are shorter and efficiency maintained. Constant pressure and constant
flow modes will give different retention times and peak shapes, so make sure you specify which mode should be used.

7) Water on non-polar column

With some sample types it can be un-avoidable to inject the sample in water. Be sure that the column you use is suitable for
water injections. As the column phase becomes increasingly non-polar (e.g. a DB-1), it loses the ability to adsorb the water
sufficiently and chromatography breaks down. For water injections try to use the most polar phase you can (e.g. Wax) and
accept that column life will decreases and bleed increase.

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10 COMMON GC MISTAKES

8) Not using the correct flame gas ratios

Lighting and maintaining a hydrogen / air flame relies on an optimal flow and ratio for
all the gases in the detector. See the advice in ‘My Detector Flame Won’t Light’.

9) Not capping the column during storage

The bonded stationary phase in a GC column is easily oxidized, particularly in the presence of UV light. Be sure to cap
the ends of the column to seal in inert carrier gas and stop air getting in. Store the column in a box in a dark cupboard to
minimize the amount of light energy reaching the column. This is important to stop the column degenerating on storage.

10) Not checking you have enough gas

In many labs, the gas supply is remote from the GC. Although it isn’t always easily accessible, it’s a whole lot less
inconvenient than having to repeat a run of samples because either the carrier or detector gasses ran out before the original
run was complete. Make checking the gas supplies one of the first things you do.

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SOLVENT CHOICE FOR GC INJECTION
A CRITICAL METHOD VARIABLE!

I guess we all have our ‘go to’ solvents for our work in GC, and most of the time this will be based on the availability of the
solvent and the chemical nature of our samples. Polar samples (analytes) generally need a more polar solvent (methanol
for example) and less polar analytes a less polar solvent (n-hexane or heptane for example). Sometimes we might even use
an intermediate polarity solvent when we aren’t sure of the analyte composition, ethyl acetate is a popular choice in this
instance.

I talk to many folks involved in GC and the conversations around sample preparation and the choice of ultimate sample
diluent are almost always around the chemistry of the sample (matrix) or the analyte and the requirements to properly
solubilise the sample.

But there are so many more issues to consider when choosing the appropriate sample solvent and setting some of our
critical method variables. I’ve given a short treatment of these considerations in this instalment so you might be better
informed when developing, optimising, transferring or troubleshooting your GC methods.

Sample Solvent (Diluent) and Injection Volume

The sample diluent has a direct effect on the amount of sample which can be injected into the GC under a given set of inlet
conditions.

As the sample is rapidly introduced into the GC inlet via the autosampler syringe, there is a rapid (explosive) evaporation of
the sample solvent which transfers the sample molecules into the gas phase. The degree of expansion will depend upon the
nature of the sample solvent (i.e. its expansion co-efficient), and the inlet temperature and pressure, which is dictated by the
combination of the liner size and the carrier gas flow rate through the inlet.

If the sample size (the number of microliters of sample you chose to inject) is too large, and other operating variables are
not favourable, the gas phase sample will exceed the volume of the inside of the inlet liner, and the gas phase sample will
contact the underside of the septum and ‘spill’ over into the carrier gas inlet and septum purge lines. As these lines are not
heated (other than the portions directly inside or next to the inlet), then the gas phase sample will condense, leaving some
of your analyte deposited within the pipework of your sample inlet system.

If one were to then inject a ‘blank’ solvent, under the same circumstances, the same overfilling phenomenon would
occur, and just as a wave ‘laps’ the seaweed and other detritus from a beach, some of the previously deposited sample
components within the pipework may be drawn back into the inlet and make their way into the column. We would be
presented with a mini version of the previous chromatogram which we describe as ‘carry-over’ and which is a major cause of
quantitative irreproducibility in capillary gas chromatography.
Chromatographers call this phenomenon ‘backflash’ (Figure 1).

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SOLVENT CHOICE FOR GC INJECTION – A CRITICAL METHOD VARIABLE!

Figure 1: The principles of sample ‘backflash’.

A – the solvent volume is too large to be contained in the inlet liner and ‘spills’ over into the inlet tubing.
B – The analyte condenses in an unheated region of tubing.
C – the next backflashed injection solvent vapour solubilises the deposited analyte and carries it back into the inlet and
subsequently on to the column – resulting in carry-over.

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SOLVENT CHOICE FOR GC INJECTION – A CRITICAL METHOD VARIABLE!

So – how does one decide on the proper injection volume or the operating variables which will avoid this insidious carry-over
effect?

Well we typically use software calculators to assess

the correct amount of sample to inject and the
appropriate inlet temperature and pressure.

The calculator needs to know the nature of the

solvent and its expansion co-efficient in order to
calculate the volume of gas created under a given
set of conditions, from a given volume of solvent
injected into the system.

It will also need the liner volume (easily calculated

or requested from suppliers) and the temperature
and pressure of the inlet, which of course you can
get from the GC system.

Figure 2: An example Backflash Calculator.

These calculators are very useful as they allow one to assess the required changes to the operating conditions in order to
avoid backflash, or on a more positive note, to assess how much sample can be injected without risking carry-over, if one
wants to improve the sensitivity of a method.

Further, the calculator can be used to make informed choices on the detector temperature setting required for a particular
method, alongside the general information that one might have about the boiling points of the higher boiling sample
components.

The calculator can also be used to assess the effects of increasing the head pressure (carrier gas flow), during the moment of
sample injection which constrains the expansion of the sample solvent plug, which is known as ‘pressure pulsed injection’, a
strategy which is also used to increase the volume of sample injected without risking backflash and hence analyte carry-over.

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Diluent effects on peak shape

During the initial phase of a splitless injection, the column is cool (40 – 70°C typically) and the sample solvent is allowed
to condense on the stationary phase on the inner wall of the capillary column. Due to the reduced vapour pressure
caused by the flowing carrier gas, the solvent evaporates and ‘concentrates’ the dissolved analytes into a sharp band. This
effect, known as solvent focussing, helps to overcome the very broad peak shapes associated with splitless injection into
a hot oven, caused by the prolonged time taken to move the sample vapour from the inlet to the column under splitless
conditions.

The peak focussing effects rely upon the solvent forming a contiguous (uninterrupted) film on the inner wall of the capillary
column. If the polarity of the column stationary phase is not well matched with the polarity of the sample diluent, this film
formation can fail and ‘pooling’ of solvent can occur which results in a non-contiguous film and very poor peak shape.

These effects along with the resulting chromatograms can be seen in Figure 3.

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SOLVENT CHOICE FOR GC INJECTION – A CRITICAL METHOD VARIABLE!

These effects can also occur to a lesser extent in split injection, however they are typically much less severe.

Typically one should avoid extremes such as using methanol as a sample diluent with non-polar GC stationary phases such
100% polydimethylsiloxane or n-hexane as a sample diluent when using polar phases such as waxes. However, minor
effects can also be seen when using intermediate polarity phases or solvents and one should take care to match the solvent
polarity with that of the stationary phase.

So, the next time your reach for the solvent bottles to dissolve or reconstitute your sample prior to loading it into the GC vial
– just stop a moment and run through the considerations above. Make an informed solvent choice – your chromatography
will be all the better for it!

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GC INLET MAINTENANCE... HAVE YOU REALLY
HEARD IT ALL BEFORE?

Many troubleshooting investigations in chromatography often don’t lead to a single causal factor. Often, the reason for
problems or lack of method robustness are related to many small ‘contributory factors’ and this is particularly true of the
problems associated with sample introduction in capillary Gas Chromatography.

I often find that, whilst most folks have a fair idea of what constitutes a good routine maintenance program for GC Split /
Splitless inlets, the reasons for the routine are poorly understood. So, to add some deeper understanding to the problems
associated with poor inlet maintenance, here is a quick multi-media blog on GC Inlet Maintenance.

Septa:
Allows the sample syringe to enter the inlet and make the injection without depressurising the inlet or interrupting the
carrier gas flow.

Problems:
Out gassing - Septa are made from plasticised rubber or silicon and the plasticiser materials or silicon components ‘out-
gas’ giving rise to increased baseline noise or the ‘hedgehog’ baseline appearance one associates with the elution of a
homologous series of analytes. This is typically overcome by a gas which flows across the underside of the septum inside
the inlet to carry away these outgassing products. This is called the ‘septum purge’ or ‘septum flush’ gas flow, and has a
typical flow rate of a few mL/min.

Figure 1: Typical septum bleed profiles from splitless and split injections.

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GC INLET MAINTENANCE... HAVE YOU REALLY HEARD IT ALL BEFORE?

Septa ‘core’ or split through prolonged use, if the incorrect syringe point style is used or if the septum nut, which holds it in
place, is over tightened, is badly fitting or if the septum is the incorrect size.

Figure 2: Coring of septa following repeated injections.

Figure 3: Needle tip styles such as type 5 cause less coring than type 3.

If the septum is split or cored, then the inlet may leak during the injection phase. With very badly cored septa, the carrier
will leak as the inlet pressure is increased to maintain constant flow during the thermal gradient.

Septa ‘stick’ to inlets leaving behind material on the metal surfaces of the inlet, causing inlet sealing problems and bleed.

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What you see:

From shards of septum which have fallen into the inlet or from a system where the septum purge flow is too low or not
working, you will see the out-gassing products of rubber and plasticiser which are usually homologous series which cause
noisy, rising and ‘hedgehog’ type baselines. The same goes for septa which leave residues on the inlet metal surfaces if
they have become ‘stuck’ within the inlet. If you are using an MS detector – look out for the following ions in the baseline /
background which are indicative of septum bleed:

m/z 73, 207, 281, 149, 167, 279

Note that the ions at 73, 207 and 281 m/z can also arise from column bleed (polysiloxanes), however the ions at 149, 167
and 279 m/z are due to plasticisers and are particularly indicative of septum bleed. Ions at 296 and 429 indicate septum
breakdown products (rather than bleed) – usually from septum shards in within the liner which are in contact with hot
quartz or metal surfaces.

From a system which leaks during the injection phase you will see a noticeable shift in baseline position across the solvent
peak and poor peak area reproducibility.

Figure 4: Shift in baseline position after injection, indicating a leak through the septum during the injection.

Where the system cannot achieve the carrier pressures required at higher oven temperatures, the system may enter safety
shut-down mode or you will experience a large baseline shift during the analysis with widely varying retention times.

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GC INLET MAINTENANCE... HAVE YOU REALLY HEARD IT ALL BEFORE?

How to stop it happening:

Ensure you have the correct septum material for the inlet temperature. Inlet temperatures above 350 oC generally require a
special septum material. What temperature are your septa rated to? Why not go and check right now!

If you overfill the inlet with sample gas (sometimes called backflash), sample components will deposit onto the lower septum
surface. Over time these bleed into the inlet, and onto the column, causing ‘ghost peaks’ or ‘memory effects’. What old
timers like me would call ‘carry-over’. You should check that the conditions of the GC injection are compatible with the
volume and solvent used for sample injection and that the volume of gas plasma formed on sample volatilisation, doesn’t
exceed the inlet liner volume. See here for a nice downloadable tool to calculate sample gas volume (http://www.chem.
agilent.com/en-US/Technical-Support/Instruments-Systems/Gas-Chromatography/utilities/Pages/GCCalculators.aspx)
The hole within a ‘pre-drilled’ septum acts as a centre guide and prevents coring provided that the septum is held under the
correct torque.

Where the system cannot achieve the carrier pressures required at higher oven temperatures,
the system may enter safety shut-down mode or you will experience a large baseline shift
during the analysis with widely varying retention times.

Figure 5: Pre-drilled septa contain a needle guide which help to prevent coring / splitting.

Some septa have ‘non-stick’ coatings which can bleed into the column and cause
baseline noise and discrete low level interfering peaks. Use only high quality septa.

Install the septum according to your manufacturer’s recommendations – paying

special attention to the torque of the retaining nut. Too tight and the septum will
split and core much more easily. Too loose and the nut may loosen further after
repeated injection, causing loss of carrier pressure and instrument shut down.
Change the septum for each major batch of analyses, for critical or trace analyses.
Over a very short time you will have a positive financial payback.

Figure 6:
Badly fitting or lower quality septa leave residues on the inlet and ‘cookie cutter’ residues.
Image courtesy of Agilent Technologies, Santa Clara, CA, USA.

Check that the actual septum purge flow from your instrument matches the method set point or instrument readout.
Since the inception of highly reliable Electronic Pressure Control (EPC) systems, flow meters have become much less
commonplace. However EPC systems can fail, become blocked, give rise to variable or incorrect flows just like annual valves
– it really is worth checking the flow manually from time to time (perhaps as part of your PM or OQ/PV schedule).

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O-rings:
Some instrument designs feature an o-ring to isolate the carrier and spilt flow from other instrument flow paths. These
are typically fitted around the inlet liner or as a sealing ring around the underside of the septum cap and are made from
fluorocarbon or graphite.

Figure 7: Fluorocarbon o-ring seals used in certain instruments.

Other instruments will use PTFE or graphite inlet seals.

Problems:
Depending on quality, fluorocarbon o-rings can out-gas contaminating materials at higher temperatures

• The o-ring can deform and cause leaks if not held under the correct torque.
• The o-ring can stick to the liner or inlet metal surfaces, causing sealing problems.

What you see:

Discrete peaks on the baseline – typically due to the focussing of contaminants at lower over temperatures and subsequent
elution of triphenylphosphine oxide, the principal outgassing component

Figure 8: Outgassing products from o-rings can lead to discrete peaks within the GC bleed profile, primarily due to the
release of triphenylphosphine oxide

Look for 277 m/z in the mass spectrum of your background or any interfering peaks!

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GC INLET MAINTENANCE... HAVE YOU REALLY HEARD IT ALL BEFORE?

If residues of the previous o-ring remain on the liner or on the inlet metal surface, this may lead to gas flows within the inlet
leaking into one another. At worst this will lead to a safety shut down, however, the problem may be more insidious and
cause poor quantitative reproducibility.

How to stop it happening:

• Use high quality o-rings.

• Change the o-ring every time you change the liner (see below).
• Do not re-use liners or o-rings which have been stuck to the liner or inlet inner metal surface.

Liner, Packing and Inlet seals:

The liner is typically a tube of quartz glass which is used to constrain the gaseous sample so it does not contact the hot metal
surfaces inside the inlet. In some instrument designs it acts to separate the column and split flows and is designed to be
a replaceable consumable which will become contaminated with involatile sample residues over time. To facilitate sample
mixing, provide a large surface area to allow volatilisation of high boiling analytes and to prevent column contamination,
sometime the liner is packed with a plug of glass wool.

Figure 9: Quartz glass liner packed with deactivated quartz wool.

Some instrument designs have a lower seal within the inlet to allow efficient splitting of the sample, to act as a coupling
device for the analytical column and to present an inert surface to the sample, especially during splitless injection where the
analyte may be held within the liner for prolonged periods.

Figure 10: Metal liner seal.

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Problems:
Over time, the inlet liner, packing material and seal becomes contaminated with involatile sample material, which acts as a
surface to adsorb analytes through inter-molecular physico-chemical interactions such as hydrogen bonding between polar
sites.

Figure 11: Contaminated liners (left) and inlet seal (right)

Image courtesy of Agilent Technologies, Santa Clara, CA, USA.

Typically, the liner and packing materials will be constructed from quartz glass which contains a large number of surface
polar (silanol) groups. To prevent unwanted secondary interaction with the analyte, these groups are chemically ‘derivatised’
to present a much less polar, less ‘active’ surface. Over time, the increased temperature and exposure to moisture will
hydrolyse the derivatising species to the polar silanol groups and unwanted polar / polar interactions between the analytes
and the liner and packing surfaces will be possible.

Figure 12: Typical liner / packing silylation reaction.

Typically the metal seals within the inlet will also be deactivated – and the hydrolysis described above is also possible.

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GC INLET MAINTENANCE... HAVE YOU REALLY HEARD IT ALL BEFORE?

What you see:

Poor quantitative reproducibility and peak tailing are the most common forms of problem when inlets become active.

Figure 13: Analyte peak tailing caused by unwanted secondary interactions with active sites within the liner, packing material
or inlet seal.

In extreme cases, analytes may not appear within the chromatogram if they are quantitatively adsorbed within the inlet.

Sometimes, analytes are not thermally stable (pesticides, carbamates, explosives, brominated flame retardants etc.) and
will degrade with prolonged exposure to higher temperatures. The presence of glass wool within the liner, and especially in
cases where this glass wool is active in terms of polar / polar interactions, can exacerbate the thermal degradation of labile
compounds.

How to stop it happening:

• Ensure you use good quality, deactivated, liners and packing materials.
• Ensure the liner design, packing amount, density and positioning are suitable for your application.
• Ensure the liner, packing and seal are deactivated with modern deactivation process which will guarantee the highest
levels of inertness.
• Change the liner as often as is necessary. This will depend on your analytes and applications, and most importantly on
the nature of your sample matrix and the amount of sample clean-up that you do prior to analysis. Most manufacturers
recommend that the liner is changed ‘regularly’ – and you should satisfy yourself that the liner is clean and deactivated
whenever you are running large campaigns of samples, critical analyses or trace level determinations. Remember that
the o-ring should be changed with each liner change and any metal seals are also changed with every or every other liner
change, especially where analytes are thermally labile, peak tailing is occurring, analytes are particularly polar or trace
level determinations are being undertaken.

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GC INLET MAINTENANCE... HAVE YOU REALLY HEARD IT ALL BEFORE?

The split line:

A large bore (typically 1/8’’) tube which carries the split gas away from the inlet. The split line may also contain a filter or
trap filled with adsorbent material such as deactivated charcoal, which acts as a trap for volatile species and reduces the
emissions from the instrument split line vent.

Figure 14: (Left) Split line indicated by the yellow arrow. Typically a wider bore tubing which allows split gas to escape from
the inlet. (Right) Typical in-line split vent filter. Image courtesy of Agilent Technologies, Santa Clara, CA, USA.

Problems:
The split line and filter (trap) become blocked over time with an accumulation of involatile material. The speed at which the
tube and trap becomes blocked will be dictated by the number and cleanliness of samples.

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GC INLET MAINTENANCE... HAVE YOU REALLY HEARD IT ALL BEFORE?

What you see:

Contamination of the split line will result in ‘ghost peaks’ – broad baseline disturbances before or after all or certain analyte
peaks. If a blank solvent is injected some or all of the peaks of the previous injection will be present, with low response and
pronounced peak broadening.

Figure 15: Ghost peak deformations caused by, amongst other causes, re-injection of contaminants from the split line.

In extreme cases, retention times may vary, this is due to the EPC unit struggling to control and balance the various applied
pressures and resulting flows against the back pressure created within the inlet by the blocked split line.

How to stop it happening:

Most preventative maintenance routines should contain a check / clean / replace action for the split vent filter and the
split line should be removed, inspected and rinsed or replaced as necessary. For instruments with heavy usage or when
analysing large numbers of dirty samples, this action should be carried out every 6 months or more frequently if required.

GC Troubleshooting E-book Page 42

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