Mass Spectrometry

Delivered by
Dr. Azizuddin Shaikh
Assistant Professor (BPS-19)
Department of Chemistry, Federal Urdu University
Gulshan-e-Iqbal, Karachi-75300, Pakistan

12/24/2024 1
 Course Outline
Previous classical methods and latest spectroscopic techniques for
structure elucidation, History, Mass spectrometry and its
application
Mass spectrometer, Function of ionization chamber,
analyzer, detector and recorder
Mass spectrum; Molecular ion peak and determination of molecular
mass
Determination of molecular formula, Index of H-deficiency
The rule of 13
Fragmentation, Fragmentation pattern of different fuctional groups.
e.g; Alkane, Cycloalkane, Alkene, Cycloalkene, Alkyne, Aromatic
hydrocarbon, Alcohol, Phenol
Fragmentation pattern of different fuctional groups. e.g. Aldehyde,
Ketone, Carboxylic Acid, Ester, Amine, Amide, Ether etc.
Introduction to EI, CI, FI, FD and FAB; Activities of interpretation of
mass spectrum
______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 2
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Title of course: Physical Methods
(Mass spectrometry)
Course code: CHEM-761
Credit hours: 4+0 (8 units or 16 classes)
Level: MS/M.Phil. Semester-I
Lecture-15: Introduction to EI, CI, FI, FD and FAB
Prepared by: Dr. Azizuddin Shaikh
Department of Chemistry
Federal Urdu University of Arts, Science and
Technology, Gulshan-e-Iqbal, Karachi

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 3
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Additional techniques of
mass spectrometry

The following techniques of mass spectrometry may be

used for molecular mass determination if molecular ion
peak is unstable and not confirmed.
 EI (Electron ionization)
 FI (Field ionization)
 FD (Field desorption)
 CI (Chemical ionization)
 FAB (Fast atomic bombardment)

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Dr. Azizuddin
12/24/2024 Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 4
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Features of EI-MS

 Most common ionization technique.

 Classical hard ionization technique.
 For compounds having low molecular masses.
 Ionization efficient but not selective.
 Significant fragmentation.
 Inexpensive, versatile and reproducible
 sample must be relatively volatile.

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 5
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 EI-Mass Spectrometer

Sample Inlet Ion Source Ion Accelerator Mass Analyzer

Mass Spectrum Recorder Amplifier Detector

41
100
69

50

27
84
15
53
2
0
0 10 20 30 40 50 60 70 80
1-Butene, 3,3-dimethyl-

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 6
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 EI-Mass Spectrometer
Ionization Chamber

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 7
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Mass Spectrometer
Ionization Chamber

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 8
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 EI-Mass Spectrum

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 9
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 EI-Mass Spectrum

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 10
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Features of FI-MS
 Developed in 1960’s.
 Organic compounds in gas-phase can ionized
when the molecules pass near the sharp metal
anode of electric field.
 Positive electrical field is created through space
and compound in inserted at the wire.
 Less fragmentation than EI.
 Soft ionization technique.
 Molecular ion is more stable than EI.
______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 11
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 FI-Mass Spectrometer
Ionization Chamber

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 12
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Features of FD-MS
 Developed in 1970s.
 Non-volatile or thermally unstable compounds.
 Same principle as field ionization.
 Positive electrical field is created at the surface
of a metal plate as anode and compound is
placed on its surface in the solid form.
 Less fragmentation than EI.
 Molecular ion is more stable than EI.
 Soft ionization technique.
______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 13
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 FD-Mass Spectrometer
Ionization Chamber

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 14
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 FD-Mass Spectrum

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 15
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 FD-Mass Spectrum

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 16
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 FI and FD-Mass Spectrometers
Ionization Chambers

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 17
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Features of CI-MS

 Reactant gases: methane, isobutane, ammonia.

 Different fragmentation form same quasi-
molecular ion.
 Quasi-molecular ion are more stable having even
electron.
 CI is used to distinguish between isomers.
 Soft ionization.
 Fragmentation less.
______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 18
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Features of CI-MS

+
CH4 + e CH4

+ +
CH4 + CH4 CH5 + CH3

+
CH5 + M CH4 + (M -H)

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 19
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Mass spectrum of CI-MS

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 20
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 CI-Mass Spectrometer
Ionization Chamber

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 21
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Features of FAB-MS
 Soft ionization method, developed in 1980s.
 Bombarding ions are rare gases, Xe or Ar. They
are ionized and passed through an electric field.
 Sample applied in form of solution of non-volatile
liquid.
 Matrix material are glycerol, nitrobenzylic
alcohol (non polars), diethanolamine and
thioglycerol.
 Dissolve the sample.
 It is suitable for sugars.
______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 22
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 FAB-Mass Spectrometer
Ionization Chamber

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 23
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 FAB-Mass Spectrum

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 24
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Different Ionization Methods
 Electron Impact (EI - Hard method)
 small molecules, 1-1000 Daltons

 Fast Atom Bombardment (FAB – Semi-hard)

 peptides, sugars, up to 6000 Daltons

 Electrospray Ionization (ESI - Soft)

 peptides, proteins, up to 200,000 Daltons

 Matrix Assisted Laser Desorption (MALDI-Soft)

 peptides, proteins, DNA, up to 500 kD

______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 25
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan
 Different Mass Analyzers
 Magnetic Sector Analyzer (MSA)
 High resolution, exact mass
 Quadrupole Analyzer (Q)
 Low (1 amu) resolution, fast, cheap

 Time-of-Flight Analyzer (TOF)

 No upper m/z limit, high throughput

 Ion Trap Mass Analyzer (QSTAR)

 Good resolution, all-in-one mass analyzer
 Ion Cyclotron Resonance (FT-ICR)
 Highest resolution, exact mass, costly
______________________________________________________________________
Dr. Azizuddin Shaikh: Department of Chemistry, Federal Urdu University of Arts, Science 26
and Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan