Gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) are techniques used to separate and analyze volatile organic compounds. GC works by carrying samples through a column via an inert carrier gas, allowing separation based on how compounds interact with the stationary phase coating inside the column. Key components include the injector, oven, column, and detector. Common detectors include the flame ionization detector and mass spectrometer. Mass spectrometry ionizes molecules and measures mass-to-charge ratios to obtain structural information like molecular weight and elemental composition.

1. GC and GC-MS
BY- ASST. PROF. SANJAYKUMAR UCHIBAGLE,
GHRU, SAIKHEDA.

2. Gas Chromatography
• Function
• Components
• Common uses
• Chromatographic resolution
• Sensitivity

3. Function
• Separation of volatile organic
compounds
• Volatile – when heated, VOCs undergo
a phase transition into intact gas-
phase species
• Separation occurs as a result of
unique equilibria established between
the solutes and the stationary phase
(the GC column)
• An inert carrier gas carries the solutes
through the column

4. Components
• Carrier Gas, N2 or He, 1-2 mL/min
• Injector
• Oven
• Column
• Detector

5. Gas tank
Oven
Column
Injector
Syringe
Detecto
r

6. Injector
• 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

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

8. Split or splitless
• Usually operated in split mode unless
sample limited
• Chromatographic resolution depends upon
the width of the sample plug
• In splitless mode the purge valve is close for
30-60 s, which means the sample plug is
30-60 seconds
• As we will see, refocusing to a more narrow
sample plug is possible with temperature
programming

9. 0.32 mm ID
Liquid
Stationar
y phase
Mobile
phase
(Helium)
flowing at 1
mL/min
Open Tubular Capillary
Column
15-60 m in length
0.1-5 mm

10. FSOT columns
• Coated with polymer, crosslinked
– Polydimethyl soloxane (non-polar)
– Poly(phenylmethyldimethyl) siloxane
(10% phenyl)
– Poly(phenylmethyl) siloxane (50% phenyl)
– Polyethylene glycol (polar)
– Poly(dicyanoallyldimethyl) siloxane
– Ploy(trifluoropropyldimethyl) siloxane

11. Polar vs. nonpolar
• Separation is based on the vapor pressure
and polarity of the components.
• Within a homologous series (alkanes,
alcohol, olefins, fatty acids) retention time
increases with chain length (or molecular
weight)
• Polar columns retain polar compounds to a
greater extent than non-polar
– C18 saturated vs. C18 saturated methyl
ester

12. C16:0
C18:0
C18:1
C18:2
C16:1
C16:0
C18:0
C18:1
C18:2
C16:1
RT (min)
RT (min)
Polar column
Non-polar column

13. Oven
• Programmable
• Isothermal- run at one constant
temperature
• Temperature programming - Start at
low temperature and gradually ramp
to higher temperature
– More constant peak width
– Better sensitivity for components that are
retained longer
– Much better chromatographic resolution
– Peak refocusing at head of column

14. Typical Temperature Program
Time (min)
0 60
50C
220C
160C

15. Detectors
• Flame Ionization Detectors (FID)
• Electron Capture Detectors (ECD)
• Electron impact/chemical ionization
(EI/CI) Mass spectrometry

16. FIDs
• Effluent exits column and enters an
air/hydrogen flame
• The gas-phase solute is pyrolized to
form electrons and ions
• All carbon species are reduced to CH2
+
ions
• These ions collected at an electrode held
above the flame
• The current reaching the electrode is
amplified to give the signal

17. FID
• A general detector for organic
compounds
• Very sensitive (10-13 g/s)
• Linear response (107)
• Rugged
• Disadvantage: specificity

18. ECD
• Ultra-sensitive detection of halogen-
containing species
• Pesticide analysis
• Other detectors besides MS
– IR
– AE

19. Mass Spectrometry

20. What kind of info can mass spec
give you?
• Molecular weight
• Elemental composition (low MW with
high resolution instrument)
• Structural info (hard ionization or CID)

21. How does it work?
• Gas-phase ions are separated
according to mass/charge ratio and
sequentially detected

22. Parts of a Mass Spec
• Sample introduction
• Source (ion formation)
• Mass analyzer (ion sep.)
• Detector (electron multiplier tube)

23. Sample Introduction/Sources
Volatiles
• Probe/electron impact (EI),Chemical ionization
(CI)
• GC/EI,CI
Involatiles
• Direct infusion/electrospray (ESI)
• HPLC/ESI
• Matrix Assisted Laser Adsorption (MALDI)
Elemental mass spec
• Inductively coupled plasma (ICP)
• Secondary Ion Mass Spectrometry (SIMS)
– surfaces

24. EI, CI
• EI (hard ionization)
– Gas-phase molecules enter source through
heated probe or GC column
– 70 eV electrons bombard molecules forming
M+* ions that fragment in unique
reproducible way to form a collection of
fragment ions
– EI spectra can be matched to library stds
• CI (soft ionization)
– Higher pressure of methane leaked into the
source (mtorr)
– Reagent ions transfer proton to analyte

25. To mass
analyzer
filament
70 eV e-
anode
repeller Acceleration
slits
GC column
EI Source
Under high vacuum

26. EI process
• M + e- M+*
f1 f2 f3
f4
This is a remarkably reproducible process. M
will fragment in the same pattern every time
using a 70 eV electron beam

28. Ion Chromatogram of Safflower
Oil

30. CI/ ion-molecule reaction
• 2CH4 + e-  CH5
+ and C2H5
+
• CH5
+ + M  MH+ + CH4
• The excess energy in MH+ is the
difference in proton affinities between
methane and M, usually not enough
to give extensive fragmentation

31. EI spectrum of phenyl acetate

32. Mass Analyzers
• Low resolution
– Quadrupole
– Ion trap
• High resolution
– TOF time of flight
– Sector instruments (magnet)
• Ultra high resolution
– ICR ion cyclotron resonance

33. Resolution
• R = m/z/Dm/z
• Unit resolution for quad and trap
• TOF up to 15000
• FT-ICR over 30000
– MALDI, Resolve 13C isotope for a protein
that weighs 30000
– Resolve charge states 29 and 30 for a
protein that weighs 30000

34. High vs low Res ESI
• Q-TOF, ICR
– complete separation of the isotope peaks
of a +3 charge state peptide
– Ion abundances are predictable
– Interferences can be recognized and
sometimes eliminated
• Ion trap, Quad
– Unit resolution

35. MVVTLIHPIAMDDGLR
594.3
594.7
595.0
601.3
595.3
601.
0
601.7
602.0
m/z
C78H135N21O22S2
+3
Q-TOF
901.4
891.7
902.3
900.6
891.2
892.6
LCQ
R = 0.88
m/z
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100

36. Quadrupole Mass Ion Filter

37. Ion Trap

38. Time of Flight -TOF

39. Where:
•mi = mass of analyte ion
•zi = charge on analyte ion
•E = extraction field
•ti = time-of-flight of ion
•ls = length of the source
•ld = length of the field-free drift region
•e = electronic charge (1.6022x10-19 C)

40. TOF with reflectron
http://www.rmjordan.com/tt1.html

41. Sector Instruments

42. Mass accuracy
• Mass Error = (5 ppm)(201.1001)/106 =
 0.0010 amu
• 201.0991 to 201.1011 (only 1
possibility)
• Sector instruments, TOF mass
analyzers
• How many possibilities with MA = 50
ppm?
with 100 ppm?

43. Exact Mass Determination
• Need Mass Spectrometer with a high
mass accuracy – 5 ppm (sector or
TOF)
• C9H15NO4, FM 201.1001 (mono-
isotopic)
• Mass accuracy = {(Mass
Error)/FM}*106
• Mass Error = (5 ppm)(201.1001)/106 =
 0.0010 amu