Online Basic Training of GC-MS Instrumentation

and Data Analysis

By
Dr. Myo Min 1
2
Gas Chromatography Mass Spectrometry( GC-MS)
 Gas chromatography/mass
spectrometry (GC/MS)
Two powerful analytical techniques

GC MS
A separation technique A detection technique

4
 Chromatography
• Chromatography : Analytical technique that
depends on separation of components in
sample
• Sample components are separated and
detected
• Separation : Between two phases
– Stationary phase
– Mobile phase

5
 Stationary Phase and Mobile 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 !

6
 Mechanism : Adsorption
• Adsorption : Components of sample are adsorbed at
active sites of stationary phase and are eluted (carried
out) at different time based on the attractive force
between stationary phase & each individual component.
• So called :
– Gas Solid Chromatography (GSC),
– Liquid Solid Chromatography (LSC)
• Examples
– Separation of O2,N2, CO, CO2, CH4 using Molecularsive (MS-5A
or MS13X)
– Porapak Q, Haysep P, Q, N, Silica gel, etc.

7
 Mechanism : Partition
• Partition: Components are separated based on the difference
in partition ability through the stationary phase layer.
• Component that has better partition ability will be eluted
before component that has poor partition ability to the same
stationary phase
• So called :
– Gas Liquid Chromatography (GLC),
– Liquid Liquid Chromatography (LLC)
• Examples :
– Separation of C1-C14 hydrocarbons using Methyl Polysiloxane (Methyl
Silicone)
– Polyethylene glycol ,

8
 Gas Chromatography
• Gas Chromatography (GC) : Chomatography technique which
gas is used as mobile phase
• Sample will be injected into the system, Injection port where
all components are vaporized and swept into the column
• Sample components will then be separated according to the
interaction with stationary phase and eluted to detector.

Signal

Detector

Carrier
Gas
Column time

9
 Chromatogram
Signal intensity of detector

tR
Peak tR : Retention Time
t0 t0 : Dead Time of Column
h
A A : Peak Area
h : Peak Height

Time
10
 GC System Components

Regulator Detector
Moisture Trap O2 Trap
Detector Gas Cylinder
HC Trap
Injector

Column Oven

Compress Gas Cylinder

11
GC Components
13
14
15
16
17
GC Column

18
Two Types of Column

19
Packed Column

20
Capillary Column

21
Capillary Column

22
Capillary Column

23
Capillary Column

24
25
26
Inside the Column

27
Column Thickness

28
Column Thickness

29
30
31
Mass Spectrometer
Mass Spectrometry
Mass spectrometry (MS) is an analytical technique that
produces spectra of the masses of the atoms or
molecules.
Spectra are used to determine the elemental or
isotopic signature of a sample, the masses of molecules
, and to elucidate the chemical structures of molecules,
such as peptides and other chemical compounds.
Mass spectrometer works by ionizing chemical
compounds to generate charged molecules or molecule
fragments and measuring their mass-to-charge ratios.
34
35
36
37
 Reaction Gas
Ion Molecule Reaction- MS
1st Octapoles
+
Repeller + +
+ +
+
+
+
+
+

Anode
+ +
+
-
e +

M+
M
2nd Octapoles
M M M M M
+ M+
Sample Gas
M+

M+

M+
Quadrupoles
M+

M+

EM
How MS is work?
o A mass spectrometer creates charged particles
(ions) from molecules by ion source.
o Ions then fragmented.
o They travel by their mass to charge ratio (m/z)
through mass analyzer.
o Different ions have different m/z.
o Ions are then count by the detector and show
spectra.
o Compound are then identified by comparing their
spectrum with library.
We create the method to control the parts in MS
 Ion Source
• After compounds travel through the column,
they enter the MS one after another.
• The molecules are then ionized by ion source.

• The main purpose of ion source is

– Ionization of molecules.
– Fragmentation.
41
42
43
 EI MODE
• In this mode molecules are ionized by
electron beam.
• Heated Filament emits Free electrons
• The electrons have energies of 70eV which
interact with sample molecules causing
ionization.
Generation of molecular ion in EI source

M ＋ e － → M+· ＋ 2e －
45
46
47
48
49
Off-Axis in iSQ

-
Diagram showing components of MS.

ION SOURCE ANALYZER DETECTOR

Magnet
Lens 2
Filament Analytical
Quadrupole Phosphor
Repeller
Screen

Pre
Trap Lens Conversion
Quads Photo-
1 Dynode multiplier
Magnet
Focuser
Filter
Ionizer
Single Quadrupole Mass Analyzer
Electron
Multiplier
Electron Reflector

Filament
Quadrupole Mass Filter

Entrance Lens
Lens 2
Lens 1

Ion Source
GC Column
MS Sepctral Data Analysis

53
54
55
Instrumentation of GC-MS

56
 West Yangon University
Department of Chemistry

GCMS Autosampler (Trace 1300, ISQ-QD) 57

UPS
58
Helium gas Cylinder and Pressure gate
59
Gas Filteration Unit
60
GCMS Autosampler (Trace 1300, ISQ-QD)
[Video slide 7]

61
GCMS Autosampler (Trace 1300, ISQ-QD)
62
GCMS Autosampler (Trace 1300, ISQ-QD)

63
GCMS Autosampler (Trace 1300, ISQ-QD)

GC Column
64
Operation and Data Analysis

65
Instrumental Operation Technique

66
Instrument Set Up

67
68
Autosampler

69
70
71
72
73
74
75
76
77
78
One sample for Acquisition

79
 GCMS Data Analysis
Column separated compound

Figure. GC chromatogram of isolated compound from lime peel

80
Figure. Comparison of MS data between isolated
compound and Gamabufotalin (mainlib) 81
Column separated compound

Figure . GCMS chromatogram of isolated compound of mangosteen

82
Figure . Comparison of MS data between isolated compound and antipain
(nist_msms library)

83
Essential Oils

GC chromatogram of the extracted essential oils from cloves

84
 OH
O Eugenol
Formula C10H12O2, MW 164
CAS#97-53-0. Entry# 153183
Phenol, 2-methoxy-4-(2-propenyl)-

Figure. Fragmentation patterns of extracted essential oil

(8.61 min) and Eugenol from GCMS library

85
 Caryophyllene
Formula C15H24, MW 204
CAS#87-44-5. Entry# 66572
Bicyclo[7,2,0]undec-4-ene,4,11,11-trimethyl-8-methylene

Figure. Fragmentation patterns of extracted essential oil (9.36 min) and

Caryophyllene from GCMS library
86
 p-Mentha-1,8-diene
Formula C10H16, MW 136
CAS#5989-54-8. Entry# 8333
Cyclohexene, 1-methyl-4-(1-methylethenyl)-

Figure. Fragmentation patterns of extracted essential oil (9.74 min) and p-Mentha-1,8-diene from
GCMS library

87
 O

O
O

Phenol, 2-methoxy-4-(2-propenyl)-,acetate
Formula C12H14O3, MW 206
CAS#93-28-7. Entry# 25268
Phenol, 4-allyl-2-methoxy-,acetate

Figure. Fragmentation patterns of extracted essential oil (10.49 min) and Phenol, 4-allyl-2-
methoxy-,acetate from GCMS library
88
 GCMS Analysis of Extracted Essential Oil of Ginger

Figure 3.4 GC chromatogram of extracted essential oil of ginger

89
 O
-Citral
C10H16O, MW 152, CAS#141-27-5,
Entry# 3321
2,6-Octadienal, 3,7-dimethyl-(E)-

Figure 3.5 (a) Matching of fragmentation patterns of extracted essential

oil and citral from GCMS data library (at 3.88 min)
90
 -Pinene
C10H16, MW 136, CAS#127-91-3,
Entry# 65779
Bicyclo[3.1.1]heptane,6,6-dimethyl-
2-methylene

Figure 3.5 (b) Matching of fragmentation patterns of extracted essential oil and
pinene from GCMS data library (at 4.63 min)
91
 Benzene,1-(1,5-dimethyl-4-hexenyl)-4-methyl-
Formula C15H22, MW 202, CAS#644-30-4, Entry#18703
Curcumene

Figure 3.5 (c) Matching of fragmentation patterns of extracted essential oil and
curcumene from GCMS data library (at 5.34 min)
92
 Cyclohexene,1-methyl-4-(5-methyl-1-methylene-4-hexenyl)-, (S)-
Formula C15H24, MW 204, CAS#495-61-4, Entry#18703
Bisabolene

Figure 3.5 (d) Matching of fragmentation patterns of extracted essential oil and
bisabolene from GCMS data library (at 5.51 min)
93
 1,3,6,10-Dodecatetraene, 3,7,11-trimethyl-, (Z,E)-
Formula C15H24, MW 204, CAS#26560-14-5, Entry#3802
(Z,E)-Farnesene

Figure 3.5 (e) Matching of fragmentation patterns of extracted essential oil and
farnesene from GCMS data library (at 5.79 min)
94
 O

Benzenepropanoic acid, a'-dimethyl-,methyl ester

Formula C12H16O2, MW 192, CAS#25080-84-6, Entry#99348
Hydrocinnamic acid, a'a'-dimethyl-,methyl ester

Figure 3.5 (f) Matching of fragmentation patterns of extracted essential oil and hydrocinnamic
acid, dimethyl-, methyl ester from GCMS data library (at 5.95 min)
95
 O

4-(1,5-dimethylhex-4-enylcyclohex-2-enone
Formula C14H22O, MW 206, CAS#1723-80-4, Entry#36208
4-(1,5-Dimethyl-4-hexenyl)-2-cyclohexen-1-one

Figure 3.5 (g) Matching of fragmentation patterns of extracted essential oil and 4-(1,5-dimethylhex-
4-enyl) cyclohex-2-enone (6.68 min) from GCMS data library (at 6.68 min)
96
How to predict the
the chemical
structure from
fragment ions ?
97
98