Introduction to Shimadzu GC/MS

Why we need GC/MS

Typical applications of GC/MS:

Pesticide residues and pollutants in water,

agricultural products, foodstuff

Organic solvents in packaging materials, ink, etc.

Drugs of abuse in urine, blood, tablets Agriculture industry

Fatty acid contents in edible oils,
Foodfat,industry
etc.

Essential oil characterization
Forensic field

Allergens in fragrance
Environmental field

Polymer characterization
Biotechnology Fragrance industry

etc…
etc…
field
Chemical industry
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 GCMS-
GCMS-QP2010 Ultra

Auto sampler

Auto injector ( AOC-20i)

GC-2010

MS detector

GCMS Solution

Interface

3
 Gas Chromatograph-
Chromatograph-Mass
Spectrometer

Detector of GC
Injection port

Flow controller
Mass Spectrometer Gas Chromatograph

Detector Mass Ion Source

Analyzer
Interface

Vacuum System Capillary Column

GC Oven

Gas supply
(Helium)
Instrument control
Control & Data Data acquisition
System Data processing
Analyst Data storage
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 Shimadzu Capillary GC Injectors
Injector Type / Uses
Split/Splitless Injector Vaporizing / Hot injector

Wide Bore Injector Vaporizing / Hot injector

On-Column Injector (OCI) Cool injector; good for

thermally labile compounds

Programmed Temperature Cool injector; good for thermally

Vaporizing (PTV) Injector labile compounds, high boiling
compounds, and for injection of
large volume of sample
Commonly used for GC-MS
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 Split Injection

For higher
concentration Septum Purge

samples
Carrier

Split

Advantage:
 Good peak shapes
in general

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 Splitless Injection

For trace level

compounds Septum Purge*
Carrier

Good for semi-

semi-volatile Split*

samples (analyte
(analyte
boiling points are
above ~150 deg C)
* Closed before and
during injection

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 On-
On-Column Injector (OCI)

Deposit sample
directly onto the
column at low
temperature
 No sample Carrier gas

discrimination for high

boiling solutes Cooling air
 Minimize decomposition IN
of thermally unstable
solutes
Cooling air

Disadvantage:
OUT

 Faster column OCI Insert

contamination by non-
non- 8

volatile compounds
 GC Separation

Separation occurs in the column

Two phases are involved:
 Stationary phase
 Mobile phase (carrier gas)

Stationary phase resides in the column

Mobile phase moves over the stationary
phase

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 Separation in column

From
To
Injectio Column Detecto
n Port
r

From To
Injectio
n Port
Column Detecto
r

From To
Injectio Column Detecto
n Port r

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 GC-
GC-MS Ionization Methods

Electron-
Electron-impact Ionization

Chemical Ionization (Positive Chemical

Ionization)

Negative Chemical Ionization

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 Electron Impact Ionization

e- E = 70 eV e- E << 70 eV

M+ e- M+
. + 2e- M
fragmentation + + +
. M+ + +
M+ ABCD+ + N
ABCD+ Neutral e-
ABC+ +C Molecular Fragment
molecule ion ions
ABC+ BC+ + A

Characteristics & limitations

• High ionizing energy – “hard” ionization
• Extensive fragmentation – “fingerprint” of molecule (identification purpose)
• m/z value of the M+ ion gives information about the molecular weight of the
compound (identification purpose)
• Usually positive ions are analyzed
• In some cases, M+ ion does not survive fragmentation because of the high
energy involved in the process

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 EI Ionization in the MS

filament

Sample
molecule e- e- e- e-
from GC

+ + to QP
+ + analyzer
+ + through
+ + + + lenses

Fragment ions

ionization
chamber
collector
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 Ionization & fragmentation example

Ionization and fragmentation of acetone

e-
(CH3)2CO [(CH3)2CO]+ [(CH3)CO]+ CH3
MW = 58 m/z = 58 m/z = 43 m = 15
Neutral molecule Molecular ion
Fragment ion / Neutral
m= mass of ion daughter ion fragment
z= charge of ion

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 Positive Chemical Ionization

e- CH4 CH4+ CH4 C2H3+

High CH4 CH4 CH3+ CH5+
energy CH2+
electrons CH4 C2H5+C2H5
+
Primary
reagent ions Secondary
Reagent reagent ions
gas
+
Protonation MH+ M Analytes
Reaction

C2H4

Characteristics & Limitation:

• Ionization by ion-molecule reaction  lower ionizing energy  “softer” ionization
process
• Molecular ion or pseudo-molecular ion can be detected  molecular weight
• Fragmentation not as extensive – limited structural information, but simple mass
spectrum
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 Negative Chemical Ionization

Analytes Associative
Low energy
- resonance
electrons
e- CH4
MX MX capture
High
e- MX
CH4 MX
energy CH4
electrons CH4
H -
Reagent gas CH4+ CH3+ M + X
Dissociative
resonance
capture

Advantage:
• Ionization by electron-molecule interaction (low energy electrons) to form
negative ions (electron capture process)
• Selective ionization of electron-capturing molecules  higher sensitivity towards
such compounds
• Fragmentation not as extensive – limited structural information, but simple mass
spectrum
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 Why is Vacuum Necessary?

Sample ions must travel from ion source to

the detector without, or with minimum
collisions with other particles

Reduce ion-
ion-molecule reactions

Reduce background interference

Increase sensitivity

Increase filament lifetime

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 GC-
GC-MS Data

3-D

m/z

m
c tru
pe
Intensity

s
ss
Ma

Chromatogram

Retention Time

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 Example of mass spectrum identification

From this mass spectrum, the molecular weight of the

compound is determined to be 130

It can also be determined from the mass spectrum that the
compound contains 3 chlorine atoms (isotope pattern)

Since chlorine has a mass number of 35, the mass of the
remaining molecule is therefore: 130 - (35 x 3) = 25.

The fragment of a molecule with a mass of 25 is C2H (C-(C-CH).
As a result, this mass spectrum provides the identity of the
molecule as C2HCl3 (Trichloroethylene)

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Similarity (Library) Search

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 AOC-
AOC-20i & AOC-
AOC-20i+s

For Liquid Injection AOC-20i

AOC-20s

21
AOC-
AOC-5000

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 Headspace (HS) Sampling

Extraction of volatile and semi-

semi-volatile
organic compounds contained in liquid or
solid matrices, e.g. VOCs in water,
residual solvents in packaging material,
fragrances in foodstuff, etc.

How it works:
Equilibration
Incubation

2. Thermodynamic equilibration.
Concentrations of analytes in the 3. A fixed volume of
1. Sample incubation vapor phase is representative of vapor is sampled and
those in the original sample introduced into the GC 23
 SPME Sampling

Desorption
Adsorption

Analytes are adsorbed

onto the fiber coating
Fused silica fiber coated material, either from the
with adsorptive material solution or from the Analytes are thermally
is exposed to the sample headspace. desorbed from the fiber
in the sealed vial. into the GC injector.
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Direct Inlet Probe (DI)
Direct Inlet analysis is used by
introducing the sample directly to MS
(bypassing GC). Good for drug samples
or other samples that have high
molecular weight and/or thermally
unstable compounds.

DI analysis is available by simply

GCMS-QP2010 Series
inserting the probe, without removing the
column.
GC does not need to be moved.

DI analysis is possible with the GC column connected.

Spectrum acquisition is possible in EI, CI, and NCI modes.
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 Chromatogram of pesticides
for Golf Course Use using GCMS
Peak No. Name of Pesticide MW SIM
1 dichlorbos(DDVP) 220 109,79
2 trichlorofon(DEP) 256 79,109
3 etridiazole 246 211,183
4 chloroneb 206 191,206
5 mecprop-methyl ester (MCPP) 228 169,228
6 fenobucarb(BPMC) 207 121,150
7 pencycuron 328 125,180
8 besrozine 335 292,264
9 simazine(CAT) 201 201,186
10 chlorothalonil(TPN) 264 266,264
11 propyzamide 255 173,255
12 diazinon 304 179,304
13 tolclofos-methyl 300 265,267
14 terbucarb 277 220,205
15 fenitrothion(MEP) 277 277,125
16 thiobencarb 257 100,257
17 chlorpyrifos 349 199,314
18 captan 299 79,149
19 pendimethalin 281 252,162
20 methyldymron 268 107,119
21 isofenphos 345 213,121
22 isoprothiolane 290 162,290
23 napropamide 271 128,271
24 butaminfos 286 286,200
25 flutolanil 323 173,323
26 isoxathion 313 105,313
27 mepronil 269 119,269
28 pyndafenthione 340 340,199
29 iprodione 329 314,316
30 EPN 323 157,323
31 bensalide(SAP) 397 215,141
A iprodione(IBP) 288 91,204
B chloronitrofen(CNP) 317 319,317
 The Analysis Conditions of GCMS

SPE : Sep-Pak PS-2

Sampling Volume : 200mL
(standard 31 components each 100 ppb)

Flow Rate of SPE: 10 mL/min

Extraction Solvent : methylene chloride 2mL

Concentration Rate : 100 times

Injection Volume to GCMS : 1 uL

Column : DB1 (0.32mmid x 30 m)

Temp. Prog. : 50C(1 min) - 100C(20C/min) -
170C(10C/min) - 290C (5C/min)

Inj. Temp. : 250
MC of first elution group
MC of second elution group
MC of third elution group
MC of last elution group
Library search result of Diazion
Library search result of Chlorpyrifos
Mass Spectrum of Napropamide and Butamifos
36