GCMS

GCMS
Fundamentals
Fundamentals
For better understanding GCMS-QP2010
The Aims of Chemical Analysis
Qualitative Analysis:
What chemical compounds are included in the
sample ?
Quantitative Analysis:
What amount of the compounds are included in the
sample ?
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
Principle of Chromatograph
Time
Detector
Column
Injector
Sample Injection
AB
AB
B
A
B
A B
Peak A
Peak B
Comparison of Chromatography
to Flow of a River
Riverbed
Light Object
Direction of flow
Heavy Object
Stationary Phase and Mobile Phase
Strong
Weak
Mobile
Mobile
phase
phase
Mobile phase and stationary
phase contact through phase
boundary
Different solutes have different
affinities to stationary phase
and mobile phase.
Difference of moving
velocity results in separation!
Stationary
Stationary
Phase
Phase
Chromatography ChromatographChromatogram
Chromatography : Analytical method
Chromatograph : Instrument
Chromatogram : Obtained picture
Chromatographer : Analyst
Three States of Matter
and Chromatographic Methods
Solid
Liquid
gas
Stationary
Phase
Solid Liquid gas
Mobile phase and sample
Gas
Gas
chromatography
chromatography
Liquid
Liquid
chromatography
chromatography
Structure of GC (for capillarycolumn)
Disused for
GC/MS
MS in case of
GC/MS
Split unit
Injection methods of GC
Split injection
Split vent is open.
Only a part of sample is introduced to column.
Used for high concentration samples
Splitless injection
Split vent is closed
Almost 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 boiling
components. 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 commonly
used methods
GC Detectors
Good sensitivity for nitrogen compounds
FTD
Good sensitivity for phosphorous compounds and
sulfureted compounds
FPD
Good sensitivity for high electron affinity compounds
(halogenated compounds)
ECD
Organic compounds, higher sensitivity than TCD
FID
Inorganic gas Low sensitivity for organic compounds
TCD
Chromatogram
t
R
t
0
S
i
g
n
a
l

i
n
t
e
n
s
i
t
y

o
f

d
e
t
e
c
t
o
r
Time
Peak
h
A
t
R
: Retention Time
t
0
: Dead Time of Column
A : Peak Area
h : Peak Height
Qualitative Analysis for GC
Same components elute at the same retention times if
the analytical conditions are same.
Sample
Injection
Standard
Sample
(Mixed solution of
component A and B)
Unknown
Sample
Component A
Component B
Analysis of standard sample (known sample)
is required
Quantitative Analysis for GC
Peak area (height) is proportional to the amount of component
entering the detector
Standard Sample 1L
(Component A 100ppm)
Component A
Unknown Sample 1L
Component A
Peak Area : 700
Peak Area : 1000
100
Concentration
(ppm)
1000
Peak Area
700
70
What is GCMS ?
GCMS : Hyphenated instrument combining GC and MS
( Gas chromatograph mass spectrometer )
MS
GC
GC:Gas chromatograph
MS:Mass spectrometer
Data from MS (Mass Spectrum)
Chromatogram
Mass Spectrum :
Mass distribution of ions is
specific to compounds.
Consideration of the spectral
pattern gives qualitative
information.
M/Z
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 quantitation
Poor in identification
GCMS
GCMS Applications Fields - 1
Pharmaceutical
Confirmation of identity of drugs
Natural products/herbal medicines
Clinical & forensic
Determination of drugs of abuse in blood, urine or other
biological matrices
Identification of organic acids to diagnose a metabolic
disorder
Agricultural
Determination of pesticide residues in agricultural
products
GCMS Applications Fields - 2
Food & beverages
Determination of contaminants in food & beverages
Identification of volatile flavor components in
food/beverages
Identification of residual solvents in food packaging
Environmental
Determination of pesticide residues in water
Determination of volatile organic compounds in waste
water, tap water, drinking water and environment water
Analysis of volatile organic compounds in air
Determination of volatile organic compounds in soil
GCMS Applications Fields - 3
Flavor & 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 electronic
components, e.g. hard disk drive
Other...
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
Sample Injection : GC
purge
split
carrier
purge
split
column
sample
carrier
purge
split
column
sample
splitless split
carrier gas :He
purity:99.995% or greater
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 column
Capillary (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, 0.53mm
3. 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)
Interface
Interface:introduction part from GC to MS
vacuum sealing with nut and ferrule
direct interface
column
MS
high vacuum
heater
What is mass spectrometer ?
Ion source
Lens
system
Rod
system
Detector
ionization
ion
focusing
mass
separation
ion
detection
Overview of QP2010
Vacuum Pumps (TMP)
Rod System
Ion Source/
Lens System
Detector
Sample from GC
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)
Evacuation system
pressure 10
-3
-10-
4
Pa(mean free path 5m-50m)
Ion source
Lens
system
Rod
system
Detector
main
pump
Fore
pump
Comparison
Oil diffusion pump
Turbo molecular pump
Rotating 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)
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)
Column
capillary column:long glass tube(30m,60m etc) having thin
layer 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
What is ion?
Ion:atom or molecule with charge
Ions can be electrically controlled.
+
Positive ion
-
Negative ion
Ionization
Sample molecules are ionized in ion
source
Three ionization methods of GC/MS
EI (electron impact ionization)
CI (chemical ionization)
NCI (negative chemical ionization)
EI(Electron Impact)
Magnet

e
e

electrons from
filament
sample
molecules

Generation of molecular ion

Me

M
+
2e

Feature of EI
Most frequently used
ionization in GC/MS
Open ion source
Generation of fragment ions
sample
ions
GCMS-QP2010 Ion Source Unit
Double filaments
Increase productivity
High luminosity ion source
Increase sensitivity
Filaments
Ionization box
Fragmentation and spectrum
Molecule is broken up at the positions with weaker chemical bonds by electron
energy
A-B-C-D e

ABCD

(molecular ion)2e
-
ABC
+
D
+
AB
+
CD
+
A
+
BCD
+
A specific spectrum pattern can be obtained corresponding to a compound
EI spectrum is powerful tool for identification.
(Library search is available : Spectra accumulated in libraries are measured
at 70eV filament electron)
A

AB

CD

ABC

BCD

ABCD

base peak
molecular ion
fragment ions
Mass of atom and mass number
Mass of an atom is represented by unit that defines mass of
12
C as 12
(atomic mass unit ; denoted by u or amu)
Mass number : Nearest integer of atomic mass
example
mass mass number
1
H 1.00782522 1
2
H 2.01410222 2
12
C 12.00000000 12
13
C 13.00335508 13
14
N 14.00307440 14
16
O 15.99491502 16
18
O 17.99915996 18
example:
mass number of water (H
2
O)
1x2+16=18
more accurate molecular weight
1.00782522x2+15.99491502=
18.01056546
Example of Fragmentation
Methane:
For internal use
CH4+
CH3+
CH2+
CH+
Electron Impact Ionization, EI
50 60 70 80
0.0
25.0
50.0
75.0
100.0
%
43
61 45 70
88 73
50 60 70 80 90
0.0
25.0
50.0
75.0
100.0
%
70
61
45
88
43
73
89 60
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
61
70
88
O O
M
M
Ethyl Acetate
NIST data base
Electronic Accelerating Voltage,
Example of EI spectrum
m.w.78
Benzene
m.w.72
Acetone
CI (Chemical Ionization)
e

CH4
C2H5
+

MH
C2H4
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
reaction
Generation of pseudo-
molecular ions
(In case of methane as reagent gas)
Comparison between EI and CI spectrum
Methylstearate M.W. 298
EI
CI
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

-
High electron affinity atom or molecule ex: halogen)
Comparison of EIPCINCI Mass Spectrum
EI
PCI
NCI
Malathione (MW 330)
Stable Isotopes of some elements
Elements (A+2) Elements (A+1) Elements (A)
4.4%
36
S 0.8%
33
S 100%
32
S
100%
127
I
100%
31
P
100%
19
F
98.0%
81
Br 100%
79
Br
32.5%
37
Cl 100%
35
Cl
3.4%
30
Si 5.1%
29
Si 100%
28
Si
0.20%
18
O 0.04%
17
O 100%
16
O
0.36%
15
N 100%
14
N
1.08%
13
C 100%
12
C
0.015%
2
H 100%
1
H
Pay attention to
Cl and Br.
Abundance Ratios of Cl and Br.
Cl
35
Cl :
37
Cl = 100 : 32.5 3 : 1
1 1
Br Br
2
1 2 1
Br
3
1
3 3
1
3
1
Cl
Cl
2
9
6
1
Cl
3
27 27
9
1
Br
79
Br :
81
Br = 100 : 98 1 : 1
Example of Isotope Peaks
Incl. two chlorines Incl. three chlorines
Incl. a chlorine
Incl. a bromine Incl. two bromines
Mass separation(1)
m
1
+
m
2
+
m
3
+

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 radio
frequency (RF) field of
amplitude V and frequency w.
In general, for mass section U
and V are varied keeping the
ratio U/V constant.
M/Z and operation parameters
M/Z=K K:Constant
Varying V selects only specific
m/z ions.
V
r
2
w
2
U+Vcos(wt)
-U-Vcos(wt)
2r
r : radius of inscribed circle
m
1
+
m
2
+
m
3
+
m
1
/z=KV
1
/r
2
w
2
m
2
/z= KV
2
/r
2
w
2
m
3
/z= KV
3
/r
2
w
2
GCMS-QP2010
Mass Filter Unit
To
detector
detector
Pre-rod (reduce contamination of main rods, can rotate)
From
ion source
ion source
main rod
Mass Separation (2)
In fact, mass filter also transfers ions withnearby masses for a
selected mass number M.Resolution
Changing set mass mass number
continuously:
When ions with mass M enters the rod, signal
gradually increases if set mass number to rods
approaches to M from lower side. And signal is
maximum at set mass number M and decreases
above M.
The observed result (peak profile) has a width
despite that the mass has infinitesimal width
M
Mass number setting
:The measure how well we can distinguish ions
of very similar m/z values
Resolution
Two peaks at m and m+ m can be
distinguished if peak has the width of m.
m
h
h/2
m
m
Resolution : R= m / m
Specification:R>2m means m< 0.5.
Two peaks apart by unit mass can be completely
distinguished
Detector (Electron Multiplier)
Converting ions to electrical siganal
ION
Electrons
The First Dynode
The negative voltage
is applied at each
dynode. The
absolute value of
voltage becomes
smaller at the latter
dynode.
Detector system of QP2010
Converting ions to electrical siganal
Electron
Multipliers
Conversion Dynode
Noise particles
Two lenses eliminate noise particles such as neutral
molecules by focusing on only ion particles.
ION
Signal ions
The Role of Conversion Dynode
(1) Detection of negative ions
(2) Enhancing signal intensity of
ions at high mass region.
Analysis Flow of GCMS
Quantitative analysis
(SIM)
Creation of calibration curve
Quantitation of unknown samples
Qualitative analysis
(Scan)
Peak Identification
Determination of monitor mass
Data Acquisition mode of GC/MS
SCAN
Acquires 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.
Data Acquisition Mode
Scan mode
At 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
V
35
V
350
SCAN
Scan rate=Scan mass number range (amu)/Scan interval(sec)
Example: (350-35)/0.5=630
Measurement with Scan Mode
TIC
0.5sec 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)
MC ( Mass Chromatogram)
TIC
M/Z
Retention Time
Mass Spectrum

TIC
M/Z
Background subtracted spectrum
Library Search
Data Search Result
If interpretation of spectrum
is difficult, .

Library Search
Data Base NIST
about 200,000 spectra
Hints on Library Search (1)
Hit data shows no m/z 78 peak
Not correct answer
Mixed components
How to Use MC
To decide a single-component peak or a multi-
component peak
To decide target component or noise
To extract target components from many peaks
Quantitation
Single Component Peak
Same spectrum at any position of
chromatogram peak
Double - Components Peak
Making use of mass chromatogram (MC)
Mass Spectra in the double-
components peak
Signal? Noise?
Signal
Noise
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
V
112
V

SIM
SIM (Selected Ion Monitoring)
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
50 100 150 200 250 300 350 400
0
50
100
%
235
165
199
239 75 176
136 105
50
63 354 282 319
50 100 150 200 250 300 350 400
0
50
100
%
79
82
77
108
263277
53
243
380 345 173 66 113 147 209 193 87 309
Measurement with SIM
M/Z X
M/Z Y
0.2sec 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
Calibration Curve
Quantitation result
Standard sample is needed to make calibration curve for each
component.

Relative sensitivity is different according to each component.

Summary
GC/MS : Mainstream of Organic compound Analysis