This document provides an overview of gas chromatography-mass spectrometry (GC-MS). It describes how GC separates components using a carrier gas and column, while MS identifies components by mass. It discusses how the two techniques are combined via an interface, allowing both separation and identification in a single run. Key components of a GC-MS system like the gas chromatograph, interface, and mass spectrometer are also outlined.

1. Hina Qaiser
MS-1 1st Semester
Department Of Biotechnology
Lahore College For Women University

2. Gas
Chromatography
• It separates
components
of sample
Interface
• Combines
both
techniques
by removing
pressure
incompatibili
ty problem
between GC
Mass
spectrometry
• Ionise eluted
component
and separate,
identify it
according to
its mass to
charge ratio

3. Gas chromatography-mass spectroscopy (GC-MS) is a hyphenated analytical
technique
exquisitely sensitive but also specific and reliable
GC can separate volatile and semi-volatile compounds with great resolution,
but it cannot identify them.
MS provide detailed structural information on most compounds such that they
can be exactly identified, but can’t readily separate them.
3

4. Therefore, marriage of both instruments have been proposed shortly after the
development of GC in the mid-1950s.
we obtain both qualitative and quantitative information of our sample in a single
run within the same instrument
Today computerized GC/MS instruments are widely used in environmental
monitoring ,in the regulation of agriculture and food safety , and in the discovery
and production of medicine.
Continued......

5. The latter part of the column passes through a heated transfer line and ends at
the entrance to ion source where compounds eluting from the column are
converted to ions and detected according to their mass to charge m/z ratio
The sample flows through the column and the compounds comprising the
mixture of interest are separated by virtue of their relative interaction with the
coating of the column (stationary phase) and the carrier gas (mobile phase).
The sample solution is injected into the GC inlet where it is vaporized and swept
onto a chromatographic column by the carrier gas (usually helium).

6. GC-MS comprise following major block
The Gas
Chromatog
raph
Interf
ace
The Mass
Spectromet
er
A data system
is necessary to
handle results
obtained during
a sample run

7. GC-MS Instrument
The insides of the GC-MS, with the column of the gas chromatograph in the oven
on the right.

8. Gas chromatography leads to Separation of volatile organic
compounds
Separation occurs as a result of unique equilibrium established
between the solutes and the stationary phase (the GC column)
An inert carrier gas carries the solutes through the column

9. Basic Components:
Carrier Gas
Gas Controls
The Injector
The Column
Two Groups:
Packed Column
Capillary Column
The Oven
The Detector
(Mass Spectrometer)
Continued......

10.  State
• Organic compounds must be in solution for injection into the gas
chromatograph.
• The solvent must be volatile and organic (for example, hexane or
dichloromethane).
 Amount
 Depending on the ionization method, analytical sensitivities of 1 to 100 pg
per component are routine.
 Preparation
• Sample preparation can range from simply dissolving some of the sample in
a suitable solvent to extensive.

12. Hydrogen:bette
r thermal conductivity.it
reacts with unsaturated
compounds &
inflammable
Helium:excellent
thermal conductivity
it is expensive
Nitrogen:redu
ced sensitivity. It is
inexpensive
Inertness
Suitable for the detector
High purity (Better than 99.995%Better than 99.9995% for Mass Spec).
Easily available
Cheap
Should not cause the risk of fire
Should give best column performance

13. Soap Bubble Meter
Similar to Rota meter & instead of a
float, soap bubble formed indicates the
flow rate
Deliver the gas with uniform pressure/flow rate
Rota meter
Placed before column inlet
It has a glass tube with a float held on
to a spring.
The level of the float is determined by
the flow rate of carrier gas

14. A GC syringe penetrates a septum to
inject sample into the vaporization
camber
Instant vaporization of the sample,
280 C
Carrier gas transports the sample
into the head of the column
Purge valve controls the fraction of
sample that enters the column

15. Deposit the sample into the column in the narrowest
band possible
The shorter the band at the beginning of the
chromatographic process - tall narrow peaks
Gives maximum resolution and sensitivity
Therefore type of injection method and operating
conditions is critical in obtaining precise and accurate
results

16. Split or Splitless
Most common method of Injection into Capillary Columns
Most commonly misunderstood also!
Same injector hardware is used for both techniques
Electronically controlled Solenoid changes Gas Flow to determine Injector function.
Split Injection
Mechanism by which a portion of the injected
solution is discarded.
Only a small portion (1/1000 - 1/20) of sample
goes through the column
Used for concentrated samples (>0.1%)
Can be performed isothermally
Fast injection speed
Injector and septa contamination not usually
noticed
Most of the sample goes through the column
(85-100%)
Used for dilute samples (<0.1%)
Injection speed slow
Should not be performed isothermally
Controlled by solenoid valve
Requires careful optimisation

17. Splitless (100:90) vs. Split (100:1)
Injector
Syringe
Injector
Syringe
Purge valve
open
Purge valve
closed
GC column GC column
He
He

18. On Column
Injection
All of the sample is transferred to the column
Needle is inserted directly into column or into
insert directly above column
Trace analysis
Thermally labile compounds e.g Pesticides, Drugs
High molecular weight

19. Metal
(1957)
Glass
(1959)
Fused
Silica
(1979)
Aluminium
Clad
(1984)
Inert Metal
(1990)
Columns

20. Length (10m – 50m)
Internal
Diameter
(0.1mm -
0.53mm)
Liquid
Stationary
Phase
Film Thickness
(0.1um - 5um)
Polarity (Non-
polar - Polar)
Choice of phase determines selectivity
Hundred of phases available
Many phases give same separation
Same phase may have multiple brand names
Stationary phase selection for capillary columns much simpler
Like dissolves like
Use polar phases for polar components
Use non-polar phases for non-polar components

21. Choosing a Column
Internal
Diameter
Film
Thickness
Length Phase
Internal Diameter
Smaller ID’s
Good resolution of early
eluting compounds
Longer analysis times
Limited dynamic range
Larger ID’s
Have less resolution of early eluting
compounds
Shorter analysis times
Sufficient resolution for complex
mixtures
Greater dynamic range

22. Film Thickness
Amount of stationary phase coating
Affects retention and capacity
Thicker films increase retention and capacity
Standard capillary columns typically 0.25µm
0.53mm ID (Megabore) typically 1.0 - 1.5µm
The maximum amount that can be injected without significant peak distortion
Column capacity increases with :-
film thickness
temperature
internal diameter
stationary phase selectivity
If exceeded, results in :-
peak broadening
asymmetry
leaking
Column Capacity

23. Length effects
Increasing the column length increases the resolution
Doubling the column length increases resolution by the factor of 1.4 but also
increases the analysis time
Long column are employed when sample contains large number of componnets
length L = 30 m is the most common column used for many analyses (drugs, pesticides, PAHs)

24. Elutes from column collected as separate fractions after being
detected - composition measured by Mass Spectrometry.
GC equipment can be directly interfaced with rapid-scan Mass
Spectrometers.
The flow rate is usually small enough to feed directly into the
ionization chamber of the Mass Spectrometer.
Packed columns use a jet separator, which removes the carrier
gas for the analyte.

25. Increase momentum of heavier analyte molecules so that
50% or more go into the skimmer.
Lighter helium molecules are deflected by vacuum and
pumped away.
Use to identify components present in natural and
biological systems.
odor/flavor of foods – pollutants.

26. Two capillary tubes aligned with a small space between them. (1 mm)
A vacuum is created between the two tubes using a pump.
The GC effluent enters the vacuum region, those molecules which continue in the
same direction enter the second capillary tube and continue to the ion source.
The carrier gas molecules are more easily diverted from the linear path by collisions.
The analyte molecules are much larger and carry more momentum.
The surface of the separator must be inactive and a reasonably even temperature.
Prone to leaks

27. • Mass Spec. is a Microanalytical Technique used to obtain information
regarding structure and Molecular weight of an analyte
• Destructive method i.e sample consumed during analysis
• In all cases some form of energy is transferred to analyte to cause
ionisation
• In principle each Mass Spectrum is unique and can be used as a
“fingerprint” to characterise the sample
• GC/MS is a combination technique that combines the separation ability of
the GC with the Detection qualities of Mass Spec.

28. • Sample injected onto column via injector
• GC then separates sample molecules
• Effluent from GC passes through transfer line into
the Ion Trap/Ion source
• Molecules then undergo electron /chemical
ionisation
• Ions are then analysed according to their mass to
charge ratio
• Ions are detected by electron multiplier which
produces a signal proportional to ions detected

29. • Electron multiplier passes the ion current signal to
system electronics
• Signal is amplified
• Result is digitised
• Results can be further processed and displayed

31. • Sample of interest vaporised into mass spec
• Energy sufficient for Ionisation and Fragmentation
of analyte molecules is acquired by interaction with
electrons from a hot Filament
• 70 eV is commonly used
• Source of electrons is a thin Rhenium wire heated
electrically to a temp where it emits free electrons

32. Molecula
r ion
The ion obtained by the loss of an electron from
the molecule
Base
peak
The most intense peak in the MS, assigned 100%
intensity
M+ Symbol often given to the molecular ion
Radical
cation
+ve charged species with an odd number of
electrons
Fragmen
t ions
Lighter cations formed by the decomposition of
the molecular ion.
These often correspond to stable carbcations.

34. • Used to confirm molecular weight
• Known as a “soft” ionisation technique
• Differs from EI in that molecules are ionised by
interaction or collision with ions of a reagent gas rather
that with electrons
• Common reagent gases used are Methane , Isobutane
and Ammonia
• Reagent gas is pumped directly into ionisation chamber
and electrons from Filament ionise the reagent gas

35. 1) Electrons are fired at the gaseous molecules…these knock off other electrons
from some of the molecules…
2) M + electron M+ + 2e-
3) Gaseous ions are accelerated by passing through an electric field. At this stage
they can be traveling at up to 2 x 10^5 m/sec. (about 1/1000 the speed of light.
4) They then pass through an electrostatic analyzer, which selects the ions of
kinetic energy within a narrow range by using an electric field.
5) The fast moving ions now pass through the poles of electromagnet, where they
are deflected.
6) The deflected ions pass through a narrow slit and are collected on a metallic
plate connected to an amplifier. For a given strength of magnetic field, only ions
of a certain mass pass through the slit and hit the collector plate. As the ions hit
the plate they cause a current to flow through the amplifier. The more ions there
are , the larger the current.

36. • The equation governing the deflection of ions in the
magnetic field is as follows:
• r=
Where r= radius of circular path in the magnetic field
m= mass of ion
V=accelerating voltage
e=electrical charge on the ion
B=strength of strength

37. • Accelerating voltage V is kept constant
• Radius of the curvature is prop to
• Inversely prop to B
• To obtain a mass spectrum, the current through the
elctromagnet is changed at a steady rate.
• Causes the magnetic field B to change its strength &
hence allows ions of different Mass/Charge value to
pass successively through the slit.
• Mass spectrum produced plotting (ion current) against
(electromagnetic current), which is equivalent to
(relative abundance) against (mass/charge (m/e) ratio).

38. There are three main ways in which mass spectrometry is applied to the
determination of the structures of organic compounds.
1. By measuring the relative heights of the molecular ion (M) peak and the
(M+1) peak we can determine the number of carbon atoms in a molecule.
2. By measuring the accurate mass of a molecular ion we can determine its
molecular formula.
3. By identifying the fragments produced when an ion breaks up inside a
mass spectrometer we can often piece together the structure of the parent
molecule.

39. Interpretation of Mass Spectra
•The MS of a typical hydrocarbon, n-decane is shown above. The molecular ion is seen as a
small peak at m/z = 142.
•Notice the series ions detected that correspond to fragments that differ by 14 mass units,
formed by the cleave of bonds at successive -CH2- units

40. REFRENCES
Chaintreau A. Simultaneous Distillation–Extraction: From Birth to Maturity – Review Flavour and
Fragrance Journal 2001; 16(2) 136-148.
Flotron V, Houessou JK, Bosio A, Delteil C, Bermond A, Camel V. Rapid Determination of
Polycyclic Aromatic Hydrocarbons in Sewage Sludges Using Microwave-Assisted Solvent
Extraction. Comparison with Other Extraction Methods. Journal of Chromatography. A 2003;
999(1-2) 175-84.
Rice SL, Mitra S. Microwave-Assisted Solvent Extraction of Solid Matrices and Subsequent
Detection of Pharmaceuticals and Personal Care Products (Ppcps) Using Gas Chromatography–
Mass Spectrometry. Analitica Chimica Acta 2007; 589 125-132.
Hubschmann HJ. Handbook of GC-MS: Fundamentals and Applications. 2d Ed. Weinheim: Wiley-
VCH; 2009.
Laskin J, Lifshitz C. Principles of Mass Spectrometry Applied to Biomolecules. New York: John
Wiley and Sons; 2006.