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GC and GCMS Fundamentals of Instrument
Troubleshooting and Maintenance
August 1, 2016
Kirk Lokits Ph.D.
Applications Chemist
1971 5930A with Oscilloscope and Strip Chart
Timeline:
• Intel introduces first microprocessor, 4004
• IBM introduces 8” floppy disk
Page 2
2016 5977B/7890B with Sampler Tower and Tray
Page 3
Page 4
“Everything was just fine
and then this happened!”
How do I go about
TROUBLESHOOTING?”
Page 5
“Everything was just fine and then
this happened!”
Logic = Something changed (slowly or sudden)
= Something is different
Track Events – log book
-Changed column, liner, septum, syringe, etc.
-Injected samples, other method, etc.
-Did maintenance, cut column, inlet flush, etc.
Page 6
Troubleshooting Starts with Isolating the problem
There are 5 basic areas from where the problem arises
FLOW
INJECTOR
COLUMN
DETECTOR
ELECTRONICS
But of course it can always be some COMBINATION
Knowing what can & can’t cause the symptom is the key
Logical Troubleshooting
Page 7
Typical Problems of Optimized Methods becoming
Unoptimized…and the Reason Why.
• Column Installation – Correct Process
• Peak Tailing – Flow Path or Activity
• Bonus Peaks – In Sample or Back Flash (Carry Over)
• Split Peaks – Injector Problems, Mixed Solvent
• No Peaks – Wasn’t Introduced, Wasn’t Detected
• Response Changes – Activity, Injector Discrimination, Detector Problem
• Peak Fronting – Overload or Solubility Mismatch, Injector Problems
• Shifting Retention – Leaks, Column Aging, Contamination or Damage
• Loss of Resolution – Separation Decreasing, Peak Broadening
• Baseline Disturbances – Column Bleed, Contamination, Electronics
• Noisy or Spiking Baseline – Electronics or Contaminated Detector
• Quantitation Problems – Activity, Injector or Detector Problems
Page 8
Column Installation Procedure
• Install the column
• Leak and installation check
• Column conditioning
• Bleed profile
• Test mix
Page 9
Column Installation
What type of ferrule should I use?
•Graphite
•Graphite/Vespel
Self Tightening Column Nuts
Page 10
For mass spec transfer line
p/n 5190-5233
For inlet or detector
p/n 5190-6194
What to Use When?
Application Requirement
Self Tightening
Column nut with
short
Graphite/Polyimide
blend ferrule
UltiMetal Plus
Flexible Metal
ferrule
Ease of Use - finger tighten / no wrench x
Inertness for active analytes x
Installed or used hardware x
Same style ferrule at inlet and MS interface x
High temp above 350 x
Mass Spec Interface fitting x
Capillary Flow Technology device x
Pre-swage for precise height into fitting x x
Re-use of ferrule x
Page 11
Solving Shrinking Ferrule Syndrome
Page 12
Page 13
Column InstallationMeasuring the right distance
White out Septa
Page 14
Cutting The Column
Gently scribe through the polyimide coating.Do not attempt to cut the glass.
Recommended tools:Diamond or carbide tipped pencil; or sapphire cleaving tool, ceramic wafer Ocular
Do not use:Scissors, file, etc.
Page 15
Example of a Bad Cut
Page 16
Examples of Column Cuts
Good
Bad
Page 17
Column Installation
How tight is
tight?
Page 18
Overtightened Ferrule
Page 19
Column InstallationLeak Check
DO NOT USE SNOOP
Electronic leak detector
IPA/Water (50:50)
Inject a non-retained peak
Page 20
Leak and Installation CheckInject a non-retained compound vs DB-1
The peak should be sharp and symmetrical
Detector Compound
FID Methane or Butane
ECD MeCl2 (headspace or diluted)
NPD CH3CN-acetonitrile (headspace or diluted)
TCD Air
MS Air or Butane
Page 21
Non-Retained Peak Shapes
Good Installation Improper Installation orInjector Leak
Check for: -Too low of a split ratio
-Injector or septum leak
-Liner problem:
(broken, leaking, misplaced)
-Column position in injector and detector
Page 22
Column Conditioning
System must be leak free before conditioning column
Heat the column to the lower of:
Isothermal maximum temperature OR
20° to 30°C above highest operation temperature
Temperature programming is not necessary
Stop conditioning when the stable baseline is obtained:
1 to 2 hours in most cases
Page 23
Generating a Bleed Profile
Temperature program the column without an
injection*
*DB-1 30m x .32mm I.D., .25µm
Temperature program // 40°C, hold 1 min // 20°/min to 320°C, hold 10 min.
Time (min.)0 5 10 15 20 25
6000
7000
8000
9000
1.0e4
1.1e4
1.2e4
1.3e4
Page 24
Peak Tailing
INJECTOR or COLUMN is Active
-Reversible adsorption of active compounds
(-OH, -NH, -SH)
FLOW problem - dead volume, obstruction, poor installation, or severe column contamination
Miscellaneous - co-elution, polarity mismatch between phase, solute or solvent, and some compounds always tail
*Tip = Inject a light hydrocarbon, should not tail unless flow path problem.
Page 25
Bonus Peaks or Ghost Peaks
Contamination in INJECTOR, COLUMN or FLOW (carrier gas)
-Carry-over from a back flash or previous sample
-Bad tank of gas or traps have expired
-Septum bleed
*TIP = Run a blank run…it should be blank!
Ghost Peaks
Back flash
Back flash occurs
when vapor
condenses on a
cooler part of the
injector. This
condensed sample
will still have a
“headspace” which
can be swept forward
to the column and
cause ghost peaks.
Page 26
Ghost Peaks
Steps to Prevent Backflash• Reduce injection volume
• Lower inlet temperature
• Consider a large volume liner
• Pressure pulse the injection (if possible)
• Change solvents
Page 27
Page 28
Split Peaks
INJECTOR (poor sample introduction)
-Injecting the sample twice (some how?)
-Mixed sample solvent (polarity difference)
-Sample in syringe needle (manual inject)
INJECTOR (activity)
-Breakdown (not really a split peak, 2 peaks)
-Sample degradation in injector
VOLATILITY
High boilers dropping out on Cold Spots
-Transfer line temps
-Unions or fittings not tracking column temp
Page 29
Logical Troubleshooting Tips
Look and Ask…Which peaks? Early or late? Trends?
= Injection technique - erratic
Page 30
No Peaks
DETECTOR (not on or not operational)
INJECTOR (not working)
-Plugged syringe/plunger not moving
-Wrong injector (or detector)
-Huge leak (older systems)
-No carrier gas flow
NOT the COLUMN Unless…
-Broken column or No column
Page 31
A Real Troubleshooting Example
No Peaks
10 20 30 40 50
14
16
18
20
22
24
26
28
30
Page 32
Is the flame Lit?
put glass piece over FID outlet----Answer in this case, Water condensation
look at output in instrument gauge-- is the digital value greater than 0.0?
Answer in this case is approximately 16.2 pico amps
Is there flow through the column?
disconnect column from detector and measure flow with a meter
Answer in this case was YES THERE IS FLOW
Assess the observations
Flame is lit and we have flow from end of column
Hypothesis: Sample not getting on column-syringe plugged?
Take syringe out and make injection manually on a dry paper towel
Answer – towel stays dry (Syringe was clogged with septum)
Pull plunger out top, add solvent and replace plunger will usually dislodge septum particle
(should hear a little pop) If you can’t dislodge plug, Replace syringe
Reassemble the Injector & Re-inject
Logical Steps Taken to Find Peaks(most of our problems are leaks and plugs)
Page 33
Peak ResponseAll Change in Size
DETECTOR (response problem)
-Settings or flows changed
-Electronics failing
-Split ratio set incorrectly
-Wrong purge activation time
-Septum purge flow too high
-Injector temperature too low*
INJECTOR
-Leaky syringe
*Tip = Is it all of them or some of them, if all then injector or detector
Page 34
Peak ResponseSome Change in Size
INJECTOR or COLUMN is active/contaminated
-Irreversible adsorption of active compounds (-OH, -NH, -SH)
-Decomposition of sample
-Temperature Change – Discrimination
-Evaporation from sample
*Tip = If only some change, then which ones? If active compounds then
activity. If tracks volatility then cold spots or inlet discrimination.
Page 35
Peak FrontingShark Fin Shaped or Just Slight
COLUMN (contaminated)
-Overload (More pronounced with large solute and phase polarity differences)
INJECTOR
-Column installation
-Compound very soluble in injection solvent (need retention gap)
-Mixed sample solvent
OTHER
-Co-elution
-Breakdown
Page 36
Retention Time Shift
2.00
3.25
4.75
2.75
4.00
5.50
INJECTOR
-Leak in the septum
-Change in injection solvent
-Large change in sample concentration
FLOW
-Change in gas velocity
COLUMN
-Contamination
-Damaged stationary phase
-Loss of stationary phase
-Change in temperature
1.75
3.00
4.50
Page 37
min8 9 10 11
1400 ng
7 ng
Effect of Sample Overload on
Retention Time and Peak Shape
Page 38
Loss of Resolution
Resolution is a function of separation and peak width
Separation
Peak Width
Page 39
Loss of Resolution - Separation Decrease
COLUMN
-Different column temperature
-Contamination (more phase?)
-Matrix components co-eluting
-Different column phase?
Separation
Peak Width
Page 40
Loss of Resolution - Peak Broadening
FLOW
-Change in carrier gas velocity
-Make-up gas
COLUMN
-Contamination
-Phase degradation
INJECTOR (efficiency)
-Settings, Liner, Installation, etc.
Peak Width
Separation
Page 41
Baseline Disturbances
Sudden Changes, Wandering, or Drifting
COLUMN or DETECTOR
-Not fully conditioned or stabilized (electronics)
-Contamination
FLOW
-Changes in carrier and/or detector gas flows
-Valves switching, leaks
WANDER
DRIFT
Page 42
Noisy Baseline
FLOW
-Contaminated gas
-Incorrect detector settings
COLUMN
-Bleed if at high temperature
-In detector flame (poor installation)
MILD
SEVERE
DETECTOR
-Air leak - ECD, TCD
-Electronics malfunction
Page 43
Spiking Baseline
DETECTOR
-Particles entering the detector
-Random: poor connection
-Regular: nearby "cycling" equipment (electronics)
Page 44
Quantitation Problems
DETECTOR
-Poor stability (electronics) or Baseline disturbances (contamination)
-Outside detector's linear range or wrong settings
Activity (adsorption) in INJECTOR or COLUMN
INJECTOR
-Technique, settings, conditions
-Syringe worn
OTHER
-Co-elution
-Matrix effects
-Sample evaporation – leaky vials
-Sample decomposition
Page 45
TROUBLESHOOTING “TOOLS”
Bleed Profile: baseline problems
Inject a non-retained peak: peak shape problems
Test mix: all problems
Isolate the components: all problems
Jumper Tube Test: baseline problems
Static Pressure Test: check for leaks
GENERATING A BLEED PROFILE
Time (min.)0 5 10 15 20 256000
7000
8000
9000
1.0e4
1.1e4
1.2e4
1.3e4
*DB-1 30m x .32mm I.D., .25µm
Temperature program // 40°C, hold 1 min //
20°/min to 320°C, hold 10 min.
Use when the column is new (for future
reference) or there is a baseline problem
Page 46
Good Installation Improper Installation orInjector Leak
Potential problems:
Injector or septum leak
Too low of a split ratio
Liner problem(broken, leaking, misplaced)
Column position in injector and detector
NON-RETAINED PEAK SHAPES
Used to Check
Flowpath
Page 47
Page 48
Test Mixes
Used to determine how "good" the column is
#1
Page 49
Column Performance Summary
THEORETICAL PLATES/METER: MIN SPEC ACTUAL
COATING EFFICIENCY:
RETENTION INDEX:
PEAK HEIGHT RATIO:
MIN SPEC MAX SPEC ACTUAL
PENTADECANE
PENTADECANE
1-UNDECANOL
ACENAPHTHYLENE
4-CHLOROPHENOL/METHYL NONANOATE
4-PROPYLANILINE/METHYL NONANOATE
0.83
1.14
1371.04 1372.04 1371.43
1459.34 1460.34 1459.53
3900 4389
90.0 95.5
COMPOUNDIDENTIFICATION
RETENTION TIME(T )R
PARTITION RATIO
(k)
PEAK WIDTH(W 1/2)
1,6-HEXANEDIOL
4-CHLOROPHENOL
METHYL NONANOATE
4-PROPYLANILINE
TRIDECANE
1-UNDECANOL
ACENAPHTHYLENE
PENTADECANE
Approximately 5-10 ng on column
(t )o
2.51
2.95
3.21
3.81
4.20
5.52
8.00
9.58
0.9
1.3
1.5
1.9
2.2
3.3
5.2
6.4
0.019
0.022
0.022
0.026
0.027
0.036
0.053
0.062
1.29
PART NO:
COLUMN I.D. NO.:
LIQUID PHASE:
FILM THICKNESS:
COLUMN DIMENSIONS:
m X mm
TEMPERATURE LIMITS:
C TO C
1225032
3303121
DB-5
0.25 µm
30 0.252
-60° 325° ( C PROGRAM)350°
TEST MIXUsed to determine how “good” the column is or if the problem is related to
the chemical properties of the analytes.
TEST TEMPERATURE: C135°
CARRIER GAS: ( )1.2(H )2 38.7
INJECTION: SPLIT ANALYST: ERIK
cmsec min
mL
RETENTION TIME (MIN)
Max.Bleed10.0 pA
325
9.0 pA
135
0 5
Page 50
Page 51
Test Mixture Components
Compounds
Hydrocarbons
FAME’s, PAH’s
Alcohols
Acids
Bases
Purpose
Efficiency
Retention
Retention
Activity
Acidic Character
Basic Character
Page 52
Own Test Mixture
• More specific to your application
• Selective detectors
• Concentrations specific to your application
• Use same instrument conditions
• Easiest to simply inject a calibration standard
• Store for future measure of column performance
ISOLATE THE COMPONENTS
Put in a known good column
Move column to a different GC, inlet or detector
Simplify the system:
• example - Direct injection instead of P&T sample introduction
Page 53
JUMPER TUBE TESTPurpose
Helps to locate the source of contamination or noise
Isolates GC components
Page 54
JUMPER TUBE TEST Isolate the Detector
Remove column from the detector
Cap detector and turn on
Blank run
Page 55
JUMPER TUBE TEST Isolation of Detector - Results
Detector is the problem
Detector OK
Page 56
JUMPER TUBE TEST Isolate the Injector
Connect the injector and detector
1-2 meters deactivated fused silica tubing
Turn on carrier gas
Blank run
Page 57
JUMPER TUBE TEST Isolate the Injector - Results
Injector OK
Injector, lines or carriergas contaminated
Page 58
JUMPER TUBE TEST Isolate the Column
Reinstall the column
Setup as before
Blank Run
Page 59
JUMPER TUBE TEST Isolate the Column - Results
Problem returns: It’s the column
Problem gone: Previous leak, solid debris, or installation
problem
Page 60
STATIC PRESSURE CHECK
Checks for Leaks in Injector or Gas Lines
Seal all injector outlets
Supply pressure from gas cylinder
up to 20psi higher than analysis
Turn off cylinder
Page 62
Common Causes of Column Performance
Degradation and or Short Column Life
• Physical damage to the polyimide coating
• Thermal damage
• Oxidation (O2 damage)
• Chemical damage by samples
• Contamination
Page 63
Physical Damage to The Polyimide Coating
• The smaller the tubing diameter, the more flexible it is.
• Avoid scratches and abrasions
• Immediate breakage does not always occur upon physical damage
Page 64
NOT what you want your column to look like!
Page 65
Thermal Damage
Degradation of the stationary phase is increased at higher temperatures. Breakage along the polymer backbone.
Dimethylpolysiloxane
CH3 CH3CH3
CH3 CH3CH3
O
Si SiSi
OOO
Page 66
Thermal DamageWhat To Do If It Happens
• Disconnect column from detector
• “Bake out” overnight at isothermal limit
• Remove 10-15 cm from column end
Page 67
Thermal Damage
• Rapid degradation of the stationary phase
caused by excessively high temperatures
Isothermal limit = Indefinite time
Programmed limit = 5-10 minutes
• Temporary "column failure" below lower
temperature limit
Page 68
Oxidation (O2 Damage)
Oxygen in the carrier gas rapidly degrades the stationary phase. The damage is accelerated at higher temperatures. Damage along the polymer backbone is irreversible.
Dimethylpolysiloxan
e
CH3 CH3CH3
CH3 CH3CH3
O
Si SiSi
OOO
O2
Group/Presentation Title
Agilent Restricted
Page 69
Oxygen DamageWhat To Do If It Happens
•Rapid damage to the column
•Usually results in irreversible column damage
Page 70
How to Prevent Column Damage by Oxygen
• High quality carrier gas (4 nine's or greater)
• Leak free injector and carrier lines
Change septa
Maintain gas regulator fittings
• Appropriate impurity traps
Page 71
OVEN TEMP 100
Configurations for Carrier Gas Purifiers
IndicatingMoisture Trap
High CapacityOxygen Trap
Indicating Oxygen Trap
GC
Page 72
Common Causes of Leaks
Re-use and mis-installation.
• Leak from O-ring, Gold Seal, ferrules, column nuts
• O-rings are elastomer compression fittings designed for one use, not
perfectly elastic.
• Gold seals are designed for one use, knife edge cuts into gold layer
giving leak tight seal w/o shrinkage or potential organic contaminants
from polyimide out-gassing/degradation.
• Re-using could result in overlap in seal rings, resulting in a leak.
• Over-tightening of fittings
Page 73
Leaks Due to Septum Nut
• With repeated use, conical needle guide gets
worn, out of round, and needs replacement as
septum can begin to “bulge” out, especially with
excessive tightening,
• Septa fail faster because needle is not guided with as
much precision.
• Under or Over tightening—tighten nut until c-clamp on
top stops turning, then ½ to ¾ turn more.
• Non-Agilent septa may be too thin, too thick, or out of
round like die-cut septa and may not seal as well.
• “Use Environments” that decrease lifetime, like using
non-Agilent Autosamplers (ours are precisely aligned),
manual injection, larger gauge syringes
• Replace septum nut annually for peace of mind.
Page 74
Avoid High Temperatures
Hotter temperatures degrade the phase faster
Maintain column at or below isothermal limit
Minimize time at programmable temperature limit
Lower temperature limit is performance related and
not related to phase damage
Page 75
Avoid Chemical Damage
There are more things that don’t go through the
column than do.
There are nasty things in samples.
Inorganic acids and bases will react with and
damage most stationary phases.
• i.e. HCl, H2SO4, KOH, NaOH, etc.
CONCLUSION: Don’t inject anything on the column!
- It will last much longer!
Page 76
Chemical DamageWhat To Do If It Happens
• Remove 1/2 - 1 meter from the front of the
columns
• Severe cases may require removal of up to 5
meters
Page 77
Column: DB-5ms, 30m x 0.25mm, 0.25um
Carrier: H2, 60 cm/sec, constant flow
Injector: split 1:20, 250C
Detector: FID, 320C, N2 makeup gas
Oven: 40C for 0.75 min, 40-325C at 20C/min, 325C for 30 min
Red: WD-40
Blue: system blank
Contamination of system by residue on
fingers during column installation
Procedure:
(1) One very small drop of liquid placed on one fingertip.
(2) Fingertip was wiped with paper towel to remove as much of the offending material as possible.
(3) Lightly touched the part of the column sticking up above the ferrule.
(4) Installed column into injector.
(5) Set oven temperature to 40C.
(6) Started oven temperature program as soon as oven reached 40C.
Page 78
Column: DB-5ms, 30m x 0.25mm, 0.25um
Carrier: H2, 60 cm/sec, constant flow
Injector: split 1:20, 250C
Detector: FID, 320C, N2 makeup gas
Oven: 40C for 0.75 min, 40-325C at 20C/min, 325C for 30 min
Red: liquid soap
Blue: system blank
Contamination from Liquid Soap
Procedure:
(1) One very small drop of liquid placed on one fingertip.
(2) Fingertip was wiped with paper towel to remove as much of the offending material as possible.
(3) Lightly touched the part of the column sticking up above the ferrule.
(4) Installed column into injector.
(5) Set oven temperature to 40C.
(6) Started oven temperature program as soon as oven reached 40C.
Page 79
Contamination from Hand Lotion
Column: DB-5ms, 30m x 0.25mm, 0.25um
Carrier: H2, 60 cm/sec, constant flow
Injector: split 1:20, 250C
Detector: FID, 320C, N2 makeup gas
Oven: 40C for 0.75 min, 40-325C at 20C/min, 325C for 30 min
Procedure:
(1) One very small drop of liquid placed on one fingertip.
(2) Fingertip was wiped with paper towel to remove as much of the offending material as possible.
(3) Lightly touched the part of the column sticking up above the ferrule.
(4) Installed column into injector.
(5) Set oven temperature to 40C.
(6) Started oven temperature program as soon as oven reached 40C.
Red: hand lotion
Blue: system blank
Page 80
Contamination of system by residue on fingers
during column installation
Column: DB-5ms, 30m x 0.25mm, 0.25um
Carrier: H2, 60 cm/sec, constant flow
Injector: split 1:20, 250oC
Detector: FID, 320oC, N2 makeup gas
Oven: 40oC for 0.75 min, 40-325oC at 20oC/min,
325oC for 30 min
Red: French Fry
Blue: system blank
Procedure:
(1) Held French fry for 5 seconds.
(2) Fingertip was wiped with paper towel to remove as much of the offending material as possible.
(3) Lightly touched the part of the column sticking up above the ferrule.
(4) Installed column into injector.
(5) Set oven temperature to 40oC.
(6) Started oven temperature program as soon as oven reached 40oC.
Page 81
Tips to Maximize Septum Life,
Minimize Septum Leaks
– Use Agilent Gold Standard, HP Point, 23-26 gauge taper
syringes. The point style cores septa significantly less when
used with CenterGuide Septa. Taper minimizes septum
coring/wear.
– Use Agilent CenterGuide Septa. The molded hole
minimizes septa coring, counter-intuitive, but true.
HP-Point Style
Solid Septum CenterGuide Septum
Page 82
Easier question: What does poor inertness look like?
Symptoms of poor GC system inertness:
* Tailing peaks
* Reduced peak response
* No peak response
* Extra peaks!
* Poor linearity of a peak – usually at low
concentrations
What Does GC System Inertness Look Like?
Page 83
Possible Inertness Problem Areas
Inlet -liner, liner packing, gold seal, stainless steel
Consumables - septa, syringe, vial, caps, inserts, solvents
Column
GC Detector - source geometry, material, column interface,
acquisition rates?
Temperatures - inlet, xfer line, source, quads, oven
Other method factors, i.e. standards & sample preparation
Page 84
How important is each component’s inertness to
overall Flowpath Inertness?
GC Flowpath Surface Areas
l (cm) d (cm) pi
Surface Area
(cm2)
Liner 7 0.2 3.142 4.4
Seal 0.4 0.8 3.142 1.0
Column 3000 0.025 3.142 235.6
Split Liners – What’s What?
Straighttube
Straighttube withglass wool
Invertedcup
BaffleFixed glass
wool
Page 85
Page 86
Splitless Injection Liners
Liner Part No. Comments
5181-3316
Single taper, deactivated, 900L volume. Taper isolates sample
from metal seal, reducing breakdown of compounds that are
active with metals. For trace samples, general application.
5062-3587
Single taper, deactivated, with glass wool, 900L volume.
Glass wool aides volatilization and protects column. For trace
(dirty) samples.
5181-3315
Double taper, deactivated, 800L volume. Taper on inlet
reduces chance for backflash into carrier gas lines. High
efficiency liner for trace, active samples.
G1544-80730
G1544-80700
Direct connect liners, single and dual taper, deactivated.
Capillary column press fits into liner end, eliminating sample
exposure to inlet. Ultimate protection for trace, active samples.
Side hole permits use with EPC.Side hole
Page 87
•Liners become contaminated with use,
collecting non-volatiles, salts, excess reagents,
etc., or become damaged/cracked.
•Should inspect and replace liners often.
•Handle with gloves and forceps.
•Insert into or remove liners only from cool
injection ports.
•Replacing with a new liner is recommended, to
ensure reproducibility
Liner Maintenance
Page 88
What about “Baking Out” Columns?
SURE! But…
Only removes semi-volatile residues
Limit to 1-2 hours
May polymerize some contaminants
Reduces column life
Page 89
Common Care and Maintenance Scheme
1. Bake out the column for no more than 2 hours.
2. Change the Liner and cut off 6”-1ft of the inlet end of the column. (Change gold seal)
3. Cut off more column. (repeat as necessary)
4. Periodically clean the injector.
Page 90
MS Troubleshooting Process (same as GC)
1. Isolate the problem.
(Blank Run, Inject Un-retained Compound, Jumper Tube Test)
2. Change only one variable at a time.
3. Compare before/after chromatograms.
(Peak shape, response, retention, baseline rise, background, look for trends, etc.)
4. Utilize Technical Support.
Page 91
Page 92
Page 93
Page 94
Page 95
AMU gain, offsetEntrance Lens,
Repeller
Ion SourceVolume
Inlet (column)Filament
FilamentDrawout
Ion Focus
Mass axis gain, offsetoffset
Tuning Parameters - EI Inert Source
Element Voltages Effect
Filament Emission 0-315ua
Electron Energy 10-241.5 volts
Energy of electron beam
Number of electrons generated
Repeller 0 – 42.7 volts Pushes ions out of the source
Drawout Ground potential Entrance aperture to lens stack
Ion Focus 0 – 242.0 volts Relative abundance
Entrance Lens 0 – 128 mV / amu Relative abundance
Entrance Lens Offset 0 – 127.5 volts Relative abundance
AMU Gain 0 – 4095 Peak Width
AMU Offset 0 – 255 Peak Width
Guide Rod or DIF +- 650 volts Focus / Guide Ions
HED +-10,000 volts Converts ions to electrons
Electron Multiplier 0 – 3000 volts Sensitivity
Mass Axis Gain 2047 Mass assignment
Mass Axis Offset 499 Mass assignment
Electron Multiplier
HED
Guide Rod or DIF
Page 96
AMU gain, offsetEntrance Lens
Repeller
Ion SourceVolume
Inlet (column)Filament
FilamentExtractor
Ion Focus
Mass axis gain, offset
Tuning Parameters - EI Extraction Source 5977
Element Voltages Effect
Filament Emission current 0-315ua / Electron Energy 10-241.5 volts Number of electrons generated / Energy of electron beam
Ion Body -4.24 – 20 volts Reference for Electron Energy
Repeller 0 – 42.7 volts Pushes ions out of the source
Extractor -10 – 10 volts Entrance aperture to lens stack
Ion Focus 0 – 242.0 volts Relative abundance
Entrance Lens 0 – 128 mV / amu Relative abundance
Entrance Lens Offset 0 – 127.5 volts Relative abundance
AMU Gain 0 – 4095 Peak Width
AMU Offset 0 – 255 Peak Width
Guide Rod or DIF +- 650 volts Focus / Guide Ions
HED +-10,000 volts Converts ions to electrons
Electron Multiplier 0 – 3000 volts Sensitivity
Mass Axis Gain 2047 Mass assignment
Mass Axis Offset 499 Mass assignment
Electron Multiplier
HED
Guide RodIon Body
Quadrupole
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Autotune report evaluation
Typical relative abundanceBase peak should be 69 or 219
502 ≥2.4%
Proper isotope ratios1.1, 4.4, 10.1% respectively
±20%
Consistent mass peak widths ±0.05 of each other (0.48-0.65) Proper absolute abundance
Minimum usually set to
400,000-650,000 for 69
Symmetrical smooth peak shapesNo split peaks ≥10%
Total peak height
Low water and air18 to 69 ≤20%
28 to 69 ≤10%
Correct mass assignments±0.1 a.m.u.
Correct mass assignments
±0.1 a.m.u.
Appropriate EM voltage ≤3000 maximum
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Good Source Cleaning Practices
Use aluminum oxide sand powder, green sandpaper,
Bar Keepers Friend®, flexible sand sticks (LCMS), Soft Scrub®
Lightly clean flat surfaces and focus on inside surface of lens
openings
Examine repeller surface and ensure flat rounded surface
Solvent wash cleaned source parts in 1water, 2acetone or
methanol, 3dichloromethane or hexane
(don’t solvent wash ceramics or polymer insulators)
Change your filaments
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Troubleshooting Tools Needed for MS
Know good pressure readings for your system (high/rough vacuum)
Known good tune voltages of a clean well functioning system
Know your background abundances (H2O, N2, CO2, column bleed ions i.e. m/z 207)
Good column background of blank baseline of column bleed
Good chromatogram of your mid to low standard or calibrator (prefer in matrix)
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Potential MS Leak Sites
O-ring around analyzer
MS column interface connection
GC inlet
Pumping system problems
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Vacuum Leak Troubleshooting Process
Isolate the system compartments (Gas flow, GC inlet, column, MS interface, MS)
Check age of gas traps, isolate from flow path (can become saturated)
Check septa, liner O-ring, Au seal, ferrule/column installation
Use dust off and manual tune window to monitor at m/z 51 and 65
Cap column off from inlet with a septa and allow MS to pump for ~ 30 mins.
Cap off MS with solid blank ferrule
Measure the flow coming out of rough pump
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Questions…
Thank you for your attention
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