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GCMSGCMSFundamentalsFundamentals
For better understanding GCMS-QP2010
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The Aims of Chemical Analysis
Qualitative Analysis:What chemical compounds are included in thesample ?
Quantitative Analysis:What amount of the compounds are included in the
sample ?
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Measurement of Organic Compounds
Analytical Instruments for organic compounds GCHPLCGC/MSLC/MSFTIR
Tools for separation GC, HPLC
Tools for qualitative analysis MS(GC/MS, LC/MS), FTIR, NMR
Tools for quantitative analysis
GC, HPLC, GC/MS, LC/MS
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Principle of Chromatograph
Time
Detector
Column
Injector
Sample Injection
A
BAB
B
AB
A
Peak A Peak B
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Comparison of Chromatography
to Flow of a River
Riverbed
Light ObjectDirection of flow
Heavy Object
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Stationary Phase and Mobile Phase
Strong Weak
MobileMobilephasephase
Mobile phase and stationaryphase contact through phase
boundary Different solutes have different
affinities to stationary phaseand mobile phase.
Difference of movingvelocity results in separation!
StationaryStationary
PhasePhase
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Chromatography ChromatographChromatogram
Chromatography :Analytical method
Chromatograph : InstrumentChromatogram : Obtained picture
Chromatographer :Analyst
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Three States of Matter
and Chromatographic Methods
Solid
Liquid
gas
StationaryPhase
SolidLiquidgas
Mobile phase and sample
GasGas
chromatographychromatography
LiquidLiquid
chromatographychromatography
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Structure of GC (for capillarycolumn)
Disused forGC/MS
MS in case of
GC/MS
Split unit
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Injection methods of GCSplit injection
Split vent is open. Only a part of sample is introduced to column.
Used for high concentration samples
Splitless injection
Split vent is closedAlmost all amount of sample is introduced to column. Used for low concentration samples
OCI injection Samples are directly injected to column.
Used for samples including both low boiling components and high boilingcomponents. Used for thermally decomposed samples.
PTV injection Low temperature at injection port Solvent is removed at injection port.
Used for large volume injections( a few L a few tens a few hundreds L)
Most commonlyused methods
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GC Detectors
Good sensitivity for nitrogen compoundsFTD
Good sensitivity for phosphorous compounds andsulfureted compounds
FPD
Good sensitivity for high electron affinity compounds(halogenated compounds)
ECD
Organic compounds, higher sensitivity than TCDFID
Inorganic gas Low sensitivity for organic compoundsTCD
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Chromatogram
tR
t0
Signalintensityo
fdetector
Time
Peak
h
A
tR : Retention Timet0 : Dead Time of Column
A : Peak Areah : Peak Height
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Qualitative Analysis for GCSame components elute at the same retention times if
the analytical conditions are same.
Sample
Injection
Standard
Sample
(Mixed solution ofcomponent A and B)
Unknown
Sample
Component AComponent B
Analysis of standard sample (known sample)
is required
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Quantitative Analysis for GCPeak area (height) is proportional to the amount of component
entering the detector
Standard Sample 1L
(Component A 100ppm)
Component A
Unknown Sample 1LComponent A
Peak Area : 700
Peak Area : 1000
100
Concentration
(ppm)
1000Peak Area
700
70
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What is GCMS ?GCMS : Hyphenated instrument combining GC and MS
( Gas chromatograph mass spectrometer )
MS GC
GC:Gas chromatograph
MS:Mass spectrometer
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Data from MS (Mass Spectrum)
Chromatogram
Mass Spectrum :Mass distribution of ions is
specific to compounds.
Consideration of the spectral
pattern gives qualitativeinformation.
M/Z
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Good Points of GC/MS
Excellent in separation, identification and quantitation
MS (Mass Spectrometer)
Excellent in identification and quantitation
Poor in separation
GC (Gas Chromatograph)
Excellent in separation and quantitationPoor in identification
GCMS
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GCMS Applications Fields - 1Pharmaceutical
Confirmation of identity of drugs Natural products/herbal medicines
Clinical & forensic
Determination of drugs of abuse in blood, urine or otherbiological matrices
Identification of organic acids to diagnose a metabolicdisorder
Agricultural Determination of pesticide residues in agricultural
products
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GCMS Applications Fields - 2Food & beverages
Determination of contaminants in food & beverages
Identification of volatile flavor components infood/beverages
Identification of residual solvents in food packaging
Environmental Determination of pesticide residues in water
Determination of volatile organic compounds in wastewater, tap water, drinking water and environment water
Analysis of volatile organic compounds in air
Determination of volatile organic compounds in soil
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GCMS Applications Fields - 3Flavor & fragrance
Identification of fragrances used in household products,
e.g. toilet cleaner, shampoo, etc.
Polymer, plastics & rubber
Analysis of volatile residual raw materials and/or
additives in polymers Identification of polymers
Electronics & semiconductor
Identification of volatile contaminants electroniccomponents, e.g. hard disk drive
Other...
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General Sample Requirements for GC/MS Analysis
Volatility and thermal stability of the analytes
Analytes must:
have sufficient vapor pressures (volatilities) be thermally stable
at the typical GC injection port, column oven and ion source
temperatures
Suitable for analyzing organic compounds in general
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Sample Injection : GC
purge
split
carrier
purge
split
column
sample
carrierpurge
split
column
sample
splitless split
carrier gas :He
purity:99.995% or greater
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Types of Column
1. Length 0.5-5m (Max 2m)
2. Outer diameter 2-4mm
3. Filling material 0.5-25% liquid phase
(Diatom earth carrier)
4.There are many types of liquid phase.Appropriate type should be selected, because
their theoretical plate numbers are not so high.Tube
Filling material
Packed column
Capillary columnCapillary (i.d. 0.25mm, 0.5mm)
Stationary phase (Liquid coating)
1. Length 12-60m (100m on occasion)
2. Outer diameter 0.1, 0.22, 0.32, 0.53mm3. Material : fused silica, inert metal
(inert, elastic)
4. The types of liquid phase are small in number.
XX-1, 5, 10, 20
Selection of liquid phase is less important
because of high theoretical number(over 100,000)
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InterfaceInterface:introduction part from GC to MS
vacuum sealing with nut and ferrule
direct interface
columnMS
high vacuum
heater
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What is mass spectrometer ?
Ion sourceLens
system
Rod
systemDetector
ionizationion
focusing
mass
separation
ion
detection
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Overview of QP2010
Vacuum Pumps (TMP)
Rod System
Ion Source/
Lens System
Detector
Sample from GC
Vacuum
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Vacuum
- another important factor-
In only high vacuum ,
ions can move from ion source to detector.
+
ion air, water, He etc.
High vacuum ( low pressure)
+ Low vacuum ( high pressure)
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Evacuation systempressure 10-3-10-4 Pa(mean free path 5m-50m)
Ion sourceLens
system
Rod
system Detector
main
pump Fore
pump
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Comparison
Oil diffusion pump
Turbo molecular pumpRotating blade deflects gas molecules down and out the out let
Clean vacuum
Short start- up time and short shut- down time
Expensive
Heated oil from the vents collects and force down gas molecules
Inexpensive
Possibility of oil contamination
Vacuum pump (main pump)
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Single pumping and differential pumping
Differential pumping is optimum system for high flow rate
high vacuum
Ionization room Analyzing room
single pumping(QP5000series)
differential pumping(QP2010)
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Columncapillary column:long glass tube(30m,60m etc) having thinlayer of methyl silicon etc.
Inside Diameter carrier gas flow into MS
larger flow worse vacuum
I.D. of column flow
0.25mm 1-2ml/min
0.32mm 2-4ml/min
0.53mm 10-20ml/min
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What is ion?Ion:atom or molecule with charge
Ions can be electrically controlled.+
Positive ion
-Negative ion
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IonizationSample molecules are ionized in ion
source
Three ionization methods of GC/MS EI (electron impact ionization)
CI (chemical ionization) NCI (negative chemical ionization)
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EI(Electron Impact)Magnet
eee electrons from
filament
sample
molecules
Generation of molecular ion
MeM+2e
Feature of EI
Most frequently usedionization in GC/MS
Open ion source
Generation of fragment ions
sample
ions
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GCMS-QP2010 Ion Source Unit
Double filaments Increase productivity
High luminosity ion source
Increase sensitivity
Filaments
Ionization box
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Fragmentation and spectrum Molecule is broken up at the positions with weaker chemical bonds by electron
energyA-B-C-D e ABCD
(molecular ion)2e-
ABC+D+
AB+CD+
A+BCD+
A specific spectrum pattern can be obtained corresponding to a compoundEI spectrum is powerful tool for identification.
(Library search is available : Spectra accumulated in libraries are measured
at 70eV filament electron)
AD
AB
CD
ABCBCD
ABCD
base peakmolecular ion
fragment ions
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Mass of atom and mass number
Mass of an atom is represented by unit that defines mass of 12C as 12
(atomic mass unit ; denoted by u or amu)Mass number : Nearest integer of atomic mass
example
mass mass number1H 1.00782522 1
2H 2.01410222 2
12C 12.00000000 12
13C 13.00335508 13
14N 14.00307440 14
16O 15.99491502 16
18O 17.99915996 18
example:
mass number of water (H2O)
1x2+16=18
more accurate molecular weight
1.00782522x2+15.99491502=
18.01056546
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Example of Fragmentation
Methane: For internal use
CH4+
CH3+
CH2+
CH+
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Electron Impact Ionization, EI
50 60 70 800.0
25.0
50.0
75.0
100.0
%
43
6145 70
8873
50 60 70 80 900.0
25.0
50.0
75.0
100.0
%
70
61
4588
43 73
8960
70eV
14eV 40 45 50 55 60 65 70 75 80 85 m/z
0
100
200
300
400
500
600
700
800
900
Int. 43
6170
88
O O
Ethyl Acetate
NIST data base
Electronic Accelerating Voltage,
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Example of EI spectrum
m.w.78
Benzene
m.w.72
Acetone
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CI (Chemical Ionization)
e
CH4 C2H5
+
MHC2H4
Reagent gas is required
Closed type ion source ( source pressure of approx. 10Pa )
Less fragmentation ( soft ionization)
Generation of pseudo-molecular ions (e.g. hydrogenated
ion)
Effective for determination of molecular weight +
Ionization of
reagent gas
ion-molecule
reactionGeneration of pseudo-
molecular ions(In case of methane as reagent gas)
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Comparison between EI and CI spectrum
Methylstearate M.W. 298
EI
CI
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NCI (Negative Chemical Ionization)Reagent gas is required
Semi-closed type ion source ( source pressure of approx. 1Pa )Less fragmentation ( soft ionization)
High sensitivity for molecules with high electron affinity
(such as Halogenated compounds)Electron Capture Reaction
e
CH4 CH3
H
CH4
CH4
CH4
e -
High electron affinity atom or molecule ex: halogen)
Comparison of EI PCI NCI Mass Spectrum
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Comparison of EIPCINCI Mass Spectrum
EI
PCI
NCI Malathione (MW 330)
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Stable Isotopes of some elements
Elements (A+2)Elements (A+1)Elements (A)
4.4%36S0.8%33S100%32S
100%127
I
100%31P
100%19F
98.0%81Br100%79Br
32.5%37Cl100%35Cl
3.4%30Si5.1%29Si100%28Si0.20%18O0.04%17O100%16O
0.36%15N100%14N
1.08%13C100%12C
0.015%2H100%1H Pay attention toCl and Br.
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Abundance Ratios of Cl and Br.
Cl35
Cl :37
Cl = 100 : 32.5 3 : 1
1 1
Br Br2
1 2 1
Br3
13 3
1
3
1
Cl Cl2
96 1
Cl3
27 279 1
Br 79Br : 81Br = 100 : 98 1 : 1
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Example of Isotope PeaksIncl. two chlorines Incl. three chlorinesIncl. a chlorine
Incl. a bromine Incl. two bromines
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Mass separation(1)
m1+
m2+
m3+
1
1
Two opposite rods will have a
potential of +(U+Vcos(wt)) and
the other two -(U+Vcos(wt))
where U is DC voltage and
Vcos(wt) represents a radiofrequency (RF) field of
amplitude V and frequency w.
In general, for mass section U
and V are varied keeping theratio U/V constant.
M/Z and operation parameters
M/Z=K K:Constant
Varying V selects only specificm/z ions.
V
r2w2
U+Vcos(wt)
-U-Vcos(wt)
2rr : radius of inscribed circle
m1+
m2+
m3+
m1/z=KV1/r2w2
m2/z= KV2/r2w2
m3/z= KV3/r2w2
GCMS-QP2010
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Mass Filter Unit
Todetectordetector
Pre-rod (reduce contamination of main rods, can rotate)
From
ion sourceion source
main rod
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Mass Separation (2)In fact, mass filter also transfers ions withnearby masses for a
selected mass number M.Resolution
Changing set mass mass numbercontinuously:When ions with mass M enters the rod, signalgradually increases if set mass number to rodsapproaches to M from lower side. And signal ismaximum at set mass number M and decreasesabove M.
The observed result (peak profile) has a widthdespite that the mass has infinitesimal width
M
Mass number setting
:The measure how well we can distinguish ions
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:The measure how well we can distinguish ions
of very similar m/z values
ResolutionTwo peaks at m and m+ m can bedistinguished if peak has the width of m.
m
h
h/2
m
mResolution : R= m / m
Specification:R>2m means m< 0.5.
Two peaks apart by unit mass can be completely
distinguished
Detector (Electron Multiplier)
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( p )Converting ions to electrical siganal
ION Electrons
The First DynodeThe negative voltageis applied at eachdynode. Theabsolute value ofvoltage becomes
smaller at the latterdynode.
Detector system of QP2010
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y QConverting ions to electrical siganal
Electron
Multipliers
Conversion Dynode
Noise particles
Two lenses eliminate noise particles such as neutralmolecules by focusing on only ion particles.
IONSignal ions
The Role of Conversion Dynode
(1) Detection of negative ions
(2) Enhancing signal intensity of
ions at high mass region.
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Analysis Flow of GCMS
Quantitative analysis(SIM)
Creation of calibration curve
Quantitation of unknown samples
Qualitative analysis(Scan)
Peak Identification
Determination of monitor mass
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Data Acquisition mode of GC/MS
SCANAcquires mass spectra in sequence at constant intervals (eg 0.5 sec) .
All acquired mass spectra are stored in PC.
Investigation of data on PC (TIC, mass spectrum, MC etc.).Qualitative analysis / Quantitative analysis.
SIM
Detection of specific masses. Quantitative analysis.
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Data Acquisition ModeScan modeAt each chromatographic point, mass number is scanned for a mass range to obtain
a spectrum at every interval. The scan interval is to be usually set 0.5 to 1 sec.
ime
Vm/z
0.5sec 0.5sec
V35
V350
SCAN
Scan rate=Scan mass number range (amu)/Scan interval(sec)
Example: (350-35)/0.5=630
Measurement with Scan Mode
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Measurement with Scan Mode
TIC0.5sec 0.5sec 0.5sec 0.5sec 0.5sec 0.5sec 0.5sec 0.5sec 0.5sec
TIC : Total Ion Chromatogram
BG (air and breeding of liquid phase)
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MC ( Mass Chromatogram)
TIC
M/Z
Retention Time
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Mass Spectrum
TIC
M/Z
Background subtracted spectrum Library Search
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Data Search Result
If interpretation of spectrumis difficult, .
Library Search
Data Base NIST
about 200,000 spectra
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Hints on Library Search (1)
Hit data shows no m/z 78 peak
Not correct answer
Mixed components
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Single Component Peak
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Single Component Peak
Same spectrum at any position of
chromatogram peak
Double Components Peak
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Double - Components Peak
Making use of mass chromatogram (MC)
Mass Spectra in the double-
components peak
Signal? Noise?
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Signal? Noise?
Signal
Noise
Data acquisition mode
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Data acquisition mode
SIM(selected ion monitoring) mode
The SIM method is used primarily in quantitative analysis.
Only specified mass numbers are measured with SIM mode.Selection of the ion to use from the target component is very important with the SIM
method. High sensitivity analysis is possible depending on the ion selected.
Time
Vm/z
0.2sec
V112
V
V
V
SIM
SIM (Selected Ion Monitoring)
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( g)
Selecting monitoring ions of target component. Making use of mass spectrum
In general, high intensity ions with higher mass are selected
Better in quantitation
Suitable for trace analysis
50 100 150 200 250 300 350 4000
50
100%
235
165
199 23975 1761361055063 354282 319
50 100 150 200 250 300 350 4000
50
100
%
79
8277 108 263277
53243 38034517366 113 147 20919387 309
Measurement with SIM
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Measurement with SIM
M/Z X
M/Z Y0.2sec 0.2sec 0.2sec 0.2sec 0.2sec 0.2sec 0.2sec 0.2sec 0.2sec
11.0 11.5 12.0 12.5 13.0 13.5
0.5
1.0
1.5
(x100,000)
160.00 (5.43)188.10 (1.00)248.90 (82.67)285.90 (32.98)
283.90 (25.34)TIC Chlorinated Pesticide
(5ppb)
Quantitation Method
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Quantitation Method
Calibration Curve Quantitation result
Standard sample is needed to make calibration curve for eachcomponent.
Relative sensitivity is different according to each component.
Summary
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Summary
GC/MS : Mainstream of Organic compound Analysis