Fundamental Principles of GC/MS &

Introduction to Shimadzu GC/MS

Customer Support Centre
Shimadzu Asia Pacific Pte. Ltd.
Singapore
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Outline
Objective: to understand how a GC/MS works
Topics:
Gas chromatography basics
Mass spectrometry basics
Basic GC/MS data
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What is GC/MS
The technique
GC/MS stands for Gas Chromatography Mass Spectrometry, an analytical
technique which allows separation and identification of organic
compounds in a sample
GC/MS analysis starts by the separation of the compounds by using gas
chromatographic technique, which makes use of a polymeric material
contained in a column (called stationary phase) and an inert gas (called
carrier gas) flowing through the column
The separated compounds are detected and further analyzed by mass
spectrometric technique. In mass spectrometry, a compound is ionized
and the resulting ions are separated according to their mass-to-charge
ratio, and the ion abundances are measured.
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What is GC/MS
The instrument
The instrument used for gas chromatographic mass spectrometric analysis
is known as a gas chromatograph mass spectrometer (also called GC/MS)
Sample
Analysis Report
Sample
Analysis
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Why we need GC/MS
The information
By using GC/MS, we can:
Identify what compounds are contained in a sample
Determine whether certain substances/compounds are present in a sample
Determine the amount (% weight, % composition) of specified compounds in a
sample
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Why we need GC/MS
Samples for GC/MS
Strictly speaking, samples for GC/MS are organic compounds with
sufficient volatility (guideline: is in vapor form or can be turned to vapor at
400
o
C or less),
sufficient thermal stability (does not decompose on heating)
In practice, some compounds which do not fulfill the criteria above can be
made to fulfill the criteria by means of chemical reaction (derivatization),
thus making it possible for these compounds to be analyzed by GC/MS
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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
Fatty acid contents in edible oils, fat, etc.
Essential oil characterization
Allergens in fragrance
Polymer characterization
etc
Food industry Agriculture industry
Environmental field Forensic field
Biotechnology field Fragrance industry
Chemical industry
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Gas Chromatograph-Mass Spectrometer
Gas flow controller
Injection Port (Injector)
Column
Detector (MS)
Carrier Gas
Sample
Data System
Separates mixture of compounds into individual components
Interface between sample introduction device (e.g. syringe) and
column
Turns liquid sample into vapor by heating
Mixes sample vapor with carrier gas
Controls the supply of gas(es) to the GC
Two types: manual flow controller and electronic flow controller
Detects separated compounds and send signal to data system
Controls GC system (more advanced, software-based system)
Converts signal from detector into human-readable format
Data analysis (process data)
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Mass Spectrometer
Ion source
Mass analyzer
Ion detector
Turns sample molecules into fragment ions
Transmits ions to mass analyzer
Separates ions according to their mass-to-charge ratio
Measures abundance of ions
Sample
Vacuum system
Evacuates the system
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Gas Chromatograph-Mass Spectrometer
Injection port
Instrument control
Data acquisition
Data processing
Data storage
Control & Data
System
GC Oven
Capillary Column
Gas Chromatograph
Vacuum System
I on Source Mass
Analyzer
Mass Spectrometer
Detector
G
a
s

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p
p
l
y

(
H
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i
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m
)
Analyst
Interface
Detector of GC
Flow controller
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Shimadzu GC/MS
GCMS-QP2010
GCMS-QP2010S
QP2010 QP2010S
GC GC-2010 GC-2010
Ionization mode
EI, CI, NCI (dedicated
ion sources). NCI has
simulated EI and CI.
EI only
Ion source temp. Variable 100 - 260 degC Variable 100 - 260 deg C
Mass range 1.5 - 1024 a.m.u. 1.5 - 900 a.m.u.
High vacuum system
Dual TMP (65 L/s + 260
L/s)
Single TMP (65 L/s)
Low vacuum system Rotary pump Rotary pump
Maximum column flow
rate
15 mL/min 2 mL/min
Sensitivity at
installation (OFN 1 pg,
m/z 272, EI)
S/N > 60 S/N > 30
Gas Chromatograph Mass Spectrometer
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GC Components of GCMS-QP2010
GC Detector (optional)
Oven
Column
I njector
GC
C
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r
r
i
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r

G
a
s
H
y
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r
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g
e
n
A
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M
a
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Detector Gas(es) FlowController
Carrier Gas FlowController
Column
Oven
For GC/MS,
carrier gas is
normally
Helium
Electronic
Flow
Controllers
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MS Components of GCMS-QP2010
Ion Detector
Vacuum chamber
Ion source
Quadrupole mass analyzer
Direct Interface to GC
Dual TMP system
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Gas Chromatography Basics
Separation of compounds occurs inside the GC column
t
2
Mixture
t
1
Mobile
(moving)
phase
Stationary
phase
t
3
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Separation of compounds
When analytes are introduced into
the column, the molecules
distribute between the stationary
and mobile phases
The molecules in the mobile
phase are carried down the
column
Those in the stationary phase are
temporarily immobile and do not
move down the column
M
S
M = mobile phase (carrier gas)
S = stationary phase
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Separation of compounds
The molecules in the mobile
phase are carried down the
column
Those in the stationary
phase are temporarily
immobile and do not move
down the column
M
S
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Separation of compounds
Molecules in the mobile
phase re-enter the
stationary phase when they
collide with the stationary
phase
At the same time span,
molecules leave the
stationary phase and enter
the mobile phase
M
S
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Separation of compounds
The molecules in the mobile
phase are carried down the
column
The process is repeated
many many times inside the
column
While the process is
repeated, separation takes
place
M
S
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Separation of compounds
All molecules of the same
compound travel through
the column at nearly the
same rate and appear as a
band of molecules (called
sample band)
M
S
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Separation of compounds
Sample band of compound
which is less soluble in the
stationary phase moves
faster, because more of the
molecules spend more time
in the mobile phase (carrier
gas)
M
S
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From
Injection
Port
To
Detector
Retention Time =
time spent by a
compound inside the
column
Column
Separation in column
From
Injection
Port
To
Detector
Column
From
Injection
Port
To
Detector
Column
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Chromatographic Data
Analysis time
Chromatogram
Intensity
Peak area (response)
Depends on amount of sample
Retention time (measured from time of injection)
Depends on compound and analytical conditions
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Goal of Gas Chromatography
No overlap between adjacent sample bands as they exit the
column
Make each sample band travel at a different rate
Minimize the width of the sample band
Analysis time
Good chromatography
Analysis time
Poor chromatography
Coeluting peaks

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Migration rates of compounds in column (1)
Different migration rates of compounds can be achieved if these
compounds have different interaction strengths with the stationary
phase
Weaker interaction
Stronger interaction
Stationary phase
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Migration rates of compounds in column (2)
Migration rate of compounds in column
depend on:
Compound chemical structure
Stationary phase chemical structure
Column temperature
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Effect of compound chemical structure on
migration rate
M
S
M
S
GC Column GC Column
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Effect of stationary phase on migration rate
M
S
M
S
GC Column 1 GC Column 2
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Effect of column temperature on migration
rate
M
S
Lower T
M
S
Higher T
GC Column GC Column
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Sample Band Width
Sample band width depends
on:
Operating conditions
Dimensions of the column
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GC Parameters
Retention time (t
R
)
Retention time of unretained compound (t
M
)
Retention factor (k)
Distribution constant (K)
Phase ratio ()
Separation factor ()
Resolution (R)
Number of theoretical plates (N)
Height equivalent to a theoretical plate (HETP)
Carrier gas linear velocity (v)
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Retention Time (t
R
)
The time an analyte takes to travel through the column
A measure of the amount of time an analyte spends in
the column
Sum of the time spent in the stationary phase and the
mobile phase
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Retention time of an unretained compound
(t
M
)
The time an unretained compound takes to travel
through the column
Unretained compound travels down the column at the
same rate as the mobile phase (carrier gas)
Equivalent to the time a compound spends in the mobile
phase
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Retention factor (k)
Another measure of retention
Ratio of the amount of time a compound spends in the stationary
and mobile phases
A measure of retention by the stationary phase
Previously called capacity factor, or partition factor
t
R
- t
M
k =
t
M
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Distribution constant (K)
Ratio of analyte concentration in the stationary phase
and mobile phase
K is constant for a given compound, stationary phase,
and column temperature
c
S
K =
c
M
c
S
= concentration in stationary phase
c
M
= concentration in mobile phase
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Phase Ratio ()
The change in the phase ratio can be used to calculate the change
in a compounds retention, provided that the same stationary phase
and column temperature (program or isothermal) are maintained
An increase in phase ratio results in a decrease in retention (k),
since K is constant; and vice versa
r
K = k
=
2d
f
r = column radius (m)
d
f
= film thickness (m)
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Separation Factor ()
A measure of the time or distance between the maxima of two
peaks
= 1 means the two peaks have the same retention and co-elute
=
k
2
k
1
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Resolution (R)
A measure of overlap between two peaks; the higher the resolution, the
less the overlap
Separation () is only the distance between two peak maxima; resolution
takes both and the width of the peaks into account
Baseline resolution usually occurs at R = 1.50
Analysis time
Analysis time
Analysis condition 1
Analysis condition 2
Same , different R
R = 1.18
t
R2
t
R1
w
h1
+ w
h2
R = 2
t
R2
t
R1
w
b1
+ w
b2
w
h
= peak width at half peak height
w
b
= peak width at base
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Number of theoretical plates (N) or Column
Efficiency
Theoretical plates is a concept
Theoretical plates numbers are an indirect measure of peak width for a
peak at a specific retention time
Columns with high N are considered to be more efficient than those with
lower N
A column with a high N will have a narrower peak at a given retention time
Column efficiency is a function of:
Column dimensions
Type of carrier gas and its average linear velocity
Compound and its retention
t
R
w
b
t
R
w
h
N = 16
N = 5.545
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Height equivalent to a theoretical plate
(HETP or H)
Another measure of column efficiency
Small plate heights indicate higher efficiency
L
H =
N
L = column length (mm)
N = theoretical plates number
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Carrier Gas Linear Velocity (v)
Affects the
chromatographic
resolution (i.e. separation)
For each gas there is a
linear velocity where
optimum separation can
be achieved (minimum
HETP)
Van Deemter Curve
Linear Velocity (cm/s)
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