Prof. Dr. Adnan M.

Massadeh

Mass Spectrometry
PHAR 323
 • Mass Spectrometry is a powerful technique for:
1. The identification of pure compounds.
2. It can also be used for confirmation of the purity
of a sample.
3. Quantitative analysis of mixtures.
• Ions are produced from sample molecules by
bombardment with a beam of electrons.
• Organic molecules are bombarded with
electrons and converted to highly energetic
positively charged ions (fragment ions, or
daughter ions).
• The loss of an electron from a molecule leads to
a radical cation (M M.⁺).
• The molecular ion (M.⁺) commonly decomposes
to a pair of fragments, which may be either a
radical plus an ion, or a small molecule plus a
radical cation.
M.⁺ m1⁺ + m2 or m 1.⁺ + m 2

• The molecular ions, the fragment ions and the

fragment radical ions are separated by
defalcation in a variable magnetic field
according to their mass and charge, and
generate a current (the ion current) at the
collector in proportion to their relative
abundances.
• The mass spectrum consists of a series of
 Instrumentation
• The mass spectrometer performs three
essential functions:
1. For molecules are subjected to a
bombardment by a stream of high energy
electrons, converting some of the molecules
to ions. (The ions are accelerated in an
electric field).
2. The accelerated ions separated according to
their mass-to-charge ratio in a magnetic or
electric field.
3. The ions with a particular field mass-to-
charge ratio are detected by a device which
• The following Figures shows the main parts of a
mass spectrometer.
•
•
2. Ion Production in the Ionization Chamber(Ion
Source)
Organic molecules react on electron bombardment
in two ways:
An electron is captured by the molecule, giving a
radical anion. (M + e M.⁻)
An electron is removed from the molecule,
giving a radical cation. (M – e M.⁺ + 2e)
The latter is more probably by a factor of 100, and
positive-ion mass spectrometry is the result.

3. Separation of the Ions in the Analyzer (Mass

4. The Detector-Recorder.
The Detector of the most instruments consists of a
counter which produces a current that is
proportional to the number of ions which strike it.
The electron multiplier is the most common
detector.
• Through the use of electron multiplier
circuits, this circuits can be measured so
accurately that the current caused from just one
ion striking the detector to be measured.
• The signal from the detector is fed to a recorder,
which produces the mass spectrum it self.
In other words
a) The focused ion beam passes through the
collector slit to the detector.
b) The detector convert the impact of a stream of
positively charged ions into an electrical currant.
c) This must be amplified and recorded, either
graphic or digitally.
5. The Data-Handling
a. The analog signal coming from the detector is
first converted to digital from in analog-to-digital
converter and the digitized data are stored in
computer memory.
b. Computer controlled instruments produce the
mass spectral data in several forms, either as a
 Ionization Chamber
• Ionization Chamber: where the actual
ionization takes place. It is at lower pressure
than the sample inlet system.
• Some means must be found to convert
enough of the sample to the vapor state to
obtain a stream of molecules flowing into the
ionization chamber.
1. The stream of sample molecules has
entered the ionization chamber, it is
bombarded by a beam of high energy
electrons.
2. The molecule are converted to ions in this
• From the ionization chamber, the beam ion
passes through a short-free region to the
mass analyzer which is the region where the
ions are separated according to their mass-to-
charge ratio.

• Most of the sample molecules are not ionized

at all. Because they are continuously drawn off
by the vacuum pumps which are connected to
the ionization chamber.
• A diagram of a typical ionization chamber is
shown:
 Filament
• The beam of high energy electrons is emitted
from heat filament (heated to several thousand
degree Celsius).

• In normal operation the electrons have an

energy of about 70eV.

• The high energy electrons strike the stream

molecules which has been admitted from the
sample system.

• The molecules will be ionized in the sample

 Repeller Plate
• A repeller plate: it carries a +ve electrical
potential, directs the newly-created ions toward a
series of accelerating plates.
• Some of the molecules converted to –ve ions
through the absorption of electrons (by repeller
plate).

An accelerating plates
• An accelerating plates. A large potential
difference, ranging from 1to 10 Kilovolts, applied
across these accelerating plates, produces
abeam of rapidly traveling +ve ions.
The ions are directed into a uniform beam by one
 A direct probe method
• With non-volatile solids a direct probe method
of introducing the sample may be used.
1) The sample is placed on the tip of the probe,
which is then inserted through a vacuum lock
into the ionization chamber.

2) The sample is placed very close to the ionizing

beam of electrons.

3) The probe is capable of being heated, thus

causing vapor from the sample to be evolved in
close proximity to the beam of electrons.

4) A system such as this one can be used to study

samples of molecules with vapor pressures
lower than 10⁹⁻ mm Hg at room temperature.
• The kinetic energy of an accelerated ion of mass
m with velocity v is equal to:
0.5mv ² = eV
v² = 2eV/m………(1)
Where m is the mass of the ion, v is the velocity of
the ion, e is the charge on the ion, and V is the
potential difference of the ion accelerating plates.
• In the presence of a magnetic field a charged
particle will describe a curved flight path. The
equation which yields the radius of curvature of
this path is:
r = mv/eH
mv/r = eH
 v = eHr/m……….(2)
Where r is the radius of the path and His the
strength of the magnetic field.
The combination of equations 1&2 to eliminate the
velocity term: m/2 = H ²r ²/2V……(3)
Equation 3 is the important equation which
governs the behavior of an ion in the mass
analyzer potion of the spectrometer.
Quadrupole Mass Analyzer
Quadrupole mass analyzer: a set of four solids
rods is arranged parallel to the direction of ion
beam. (See the following Figure).
Quadruple Mass Analyzer
•
• Low resolution instruments have R values
ranging as high as 2000.
• Resolutions as high as 10000 may be obtained
with Quadrupole mass analyzer.

Fragmentation
• Fragmentation involves the loss of an electrically
neutral fragment.
• The most common mode of fragmentation
involves the cleavage of single bond.
 i. In this process, the odd-electron molecular
ion yields an odd electron neutral
fragment and an even-electron fragment
ion.
ii. The neutral fragment which is lost a
radical, while the fragment is of the
carbonium ion type.
iii. Cleavages which lead to the formation of
more stable carbonium ions will be favored.
iv. The ease of fragmentation to form ions
increase in the order:
CH3⁺<RCH2⁺<R2CH⁺<R3C⁺<CH2=CH-
CH2⁺<Ph-CH2⁺
Examples: of fragmentation via the cleavage of
one bond are:
[R-CH3]⁺˙ R⁺ + CH 3˙
[R-X]⁺˙ R⁺ + X˙
[R-CH2=CH-CH2]⁺˙ R˙ + [⁺CH2-CH=CH2
⁺CH2-CH=CH2]
Molecular ion(M+.) cation + radical
R-CH2CH2˙⁺CH3 RCH2CH2⁺+CH3˙ or
RCH2CH2˙ + CH3⁺
Fragmentation of a molecule depends on the
ionization potential of that molecule, non-bonding
e on O or N, IIe of C=C have less ionization
potentials than C-C bond.
•
• For branched at the branching point because of
the more stable carbocation.
CH 3
[CH 3 - CH – CH2CH3]⁺˙
CH3⁺CHCH2CH3+.CH3
2-Methylbutane M – 15 =
57m/e 52%
CH 3 CH 3
CH3 - C - CH 3]⁺˙ CH 3 - C⁺ + CH 3.
CH3 CH3
Noepentane M -15 =57m/e
100%
Question: Explain why the peak at M⁺ - 29 has
high intensity compared to the peak at M⁺ - 15 in
the mass spectrum 3-methylpentane?
Answer: carboncation (⁺C) stabilized by resonance
have high intensities.
Alkenes: CH2=CH-CH2:R CH2-CH=CH2 + ˙R
N,O,S atoms, C-C bond next to them can break
readily R-O⁺˙-CH2:CH3 R-O⁺=CH 2
+ ˙CH3
R-O:-CH2⁺
III. C-C next to C=O can break readily
R – C = O:+. R–C O:⁺ + .R
R’ R’- C.⁺ = :O:
IV.

m/e = 91 Tropylium ion

Fragmentation by cleavage of two binds:
A radical-cation (2bonds cleavage) a new
radical-cation+a neutral molecule.
Determination of Molecule Formula and
Molecular weight
For C,H,N: the naturally occurring heavier isotope
is +1 (M⁺˙ + 1) peak.
For O,S,Br,Cl: the naturally occurring heavier
Fragmentation
Example: CH 4
MWt. = 12 + (4 × 1) = 16
If (M+) is ion intensity is 100%
(M + 1) ion intensity is=(1 ×1.11) + (4 ×0.016) =
1.11+0.064 = 1.174%
Steps to be followed in calculating the molecular
formula from MS:
Nitrogen Rule:
If M⁺ is even number, the compound must contain
even number of N atoms, O included 0,2,4,6……

Odd number M⁺ is for other compounds.

M⁺ should be the highest mass in spectrum.
Other ions are due to logical loses of fragments:
M⁺ - 14 = M⁺ - CH3
M⁺ - 16 = M⁺ - O
M⁺ - 17 = M⁺ - OH or NH3
Example 1: Determine the molecular formula of the
following compounds:
M/e Intensity
42 10.0
43 0.56
44 100
73 86.1
74 3.2
75 0.2
•
Mass spectrum consists of peaks or lines of
different intensities plotted against m/e.
Example: Dodecane
 Mass Spectra
Example: N,N-diethyl methyl amine
 Mass Spectra
Example: 4-methyl-3-pentene-2-one
Example: Toluene
Examples: hexane; 2,3-dimethyl butane;
cyclohexane
 Interpretation of Mass Spectra
The mass spectrum is shown as a plot of ion a
bundance versus m/e ratio.
The most abundant ion formed in the ionization
chamber gives rise to the tallest peak in the mass
spectrum (base peak).
The relative abundances of all of the other peaks in
the spectrum are reported as a percentage of the
base peak.
The simple removal of an electron from a molecule
yields an ion whose weight is the actual molecular
weight of the original molecule.
The molecular ion obtained is the molecular ion
which is frequently symbolized by M⁺ (lifetime 10⁹⁻
• Peaks caused by ions bearing heavier isotopes
are also found in the mass spectrum (¹H and ²H,
¹²C and ¹³C etc.)
• The relative abundances of these isotopic peaks
are proportional to the abundances of the
isotope in nature.
• Besides looking for the molecular ion peak (M⁺),
one also attempts to locate M + 1 and M + 2
peaks that can be used to determine molecular
formula of the substance being studied.
• The formula for calculating the intensity of the M
+ 1 peak is :
%(M+1) = [100(M+1)/M] = 1.1 × number of C
atoms + 0.016 × number of H atoms + 0.38 ×
• The formula foe calculating the approximate
intensity of the M + 2 peak is:
%(M + 2) = [100(M + 2)/M] = 1.1 ×[(number C
atoms)²/200] + 0.016 ×[(number of H
atoms)²/200] + [(0.2 × number of O atoms)].
Example:
 Problems
1. Deduce the structure or structures which would
be consistent with the MS spectrum
2. Deduce the structure or structures which would
be consistent with the IR and MS spectra
C8 H8 O 2
Molecular Ion Mass Lost Possible
Ion Fragment
114 85 29 C2 H5
114 70 43 C3 H7
114 57 57 C4 H9
114 43 71 C5H11

• Loss of fragments which increase in mass by (i.

e. CH2) is characteristic of an unbranched
hydrocarbon chain.
n-octane C 8H18
 Molecular Ion Mass Lost Possible
Ion Fragment
120 91 29 C2 H5

120 77 43 C3 H7

• If we have the mass spectrum containing an

aromatic ring, then we should expect to find a
peak from a very stable ion, benzyl ion PhCH2,
provided the structure permitted this ion to
form. An substituted benzyl peak is found at m/
z 91, substitution will obviously change the
mass of the ion.