GC and GCMS Fundamentals of Instrument Troubleshooting and Maintenance · 2018. 4. 4. · GC and GCMS Fundamentals of Instrument Troubleshooting and Maintenance August 1, 2016 Kirk

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

“Everything was just fine

and then this happened!”

How do I go about

TROUBLESHOOTING?”

“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.

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

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

Column Installation Procedure

• Install the column

• Leak and installation check

• Column conditioning

• Bleed profile

• Test mix

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

Column InstallationMeasuring the right distance

White out Septa

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.

Example of a Bad Cut

Examples of Column Cuts

Good

Bad

Column Installation

How tight is

tight?

Overtightened Ferrule

Column InstallationLeak Check

DO NOT USE SNOOP

Electronic leak detector

IPA/Water (50:50)

Inject a non-retained peak

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

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

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

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

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.

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

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

Logical Troubleshooting Tips

Look and Ask…Which peaks? Early or late? Trends?

= Injection technique - erratic

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

A Real Troubleshooting Example

No Peaks

10 20 30 40 50

14

16

18

20

22

24

26

28

30

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)

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

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.

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

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

min8 9 10 11

1400 ng

7 ng

Effect of Sample Overload on

Retention Time and Peak Shape

Loss of Resolution

Resolution is a function of separation and peak width

Separation

Peak Width

Loss of Resolution - Separation Decrease

COLUMN

-Different column temperature

-Contamination (more phase?)

-Matrix components co-eluting

-Different column phase?

Separation

Peak Width

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

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

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

Spiking Baseline

DETECTOR

-Particles entering the detector

-Random: poor connection

-Regular: nearby "cycling" equipment (electronics)

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

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

Test Mixes

Used to determine how "good" the column is

#1

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

Test Mixture Components

Compounds

Hydrocarbons

FAME’s, PAH’s

Alcohols

Acids

Bases

Purpose

Efficiency

Retention

Retention

Activity

Acidic Character

Basic Character

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

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

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

NOT what you want your column to look like!

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

Thermal DamageWhat To Do If It Happens

• Disconnect column from detector

• “Bake out” overnight at isothermal limit

• Remove 10-15 cm from column end

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

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

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

OVEN TEMP 100

Configurations for Carrier Gas Purifiers

IndicatingMoisture Trap

High CapacityOxygen Trap

Indicating Oxygen Trap

GC

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

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.

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

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!

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

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.






Red: liquid soap

Blue: system blank

Contamination from Liquid Soap

Procedure:







Contamination from Hand Lotion






Procedure:







Red: hand lotion

Blue: system blank

Contamination of system by residue on fingers

during column installation



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.




(5) Set oven temperature to 40oC.

(6) Started oven temperature program as soon as oven reached 40oC.

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

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?

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

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

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

•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

What about “Baking Out” Columns?

SURE! But…

Only removes semi-volatile residues

Limit to 1-2 hours

May polymerize some contaminants

Reduces column life

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.

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.

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

Page 97

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

Page 98

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

Page 99

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)

Page 100

Potential MS Leak Sites

O-ring around analyzer

MS column interface connection

GC inlet

Pumping system problems

Page 101

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

Page 102

Questions…

Thank you for your attention

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GC and GCMS Fundamentals of Instrument Troubleshooting and Maintenance · 2018. 4. 4. · GC and GCMS Fundamentals of Instrument Troubleshooting and Maintenance August 1, 2016 Kirk