Prepared By:-

Abdullah Bin Queyam

ME-EIC
801151001
A Mass Spectrometer is a machine that weighs
molecules !
0 units
12 units
A Mass Spectrometer is a machine that weighs
molecules !
12 units
8 9 10 11 12 13 14 15 16
A Mass Spectrometer is a machine that weighs
molecules !
14 units
8 9 10 11 12 13 14 15 16
A Mass Spectrometer is a machine that weighs
molecules !
0 Units
8 9 10 11 12 13 14 15 16
mass
N
u
m
b
e
r

o
f

c
o
u
n
t
s

A Mass Spectrometer is a machine that weighs
molecules !
Basic Chemistry

Analytical Chemistry

Mass Spectrometry
Types of Ion Sources
EI, CI, ESI, APCI, APPI, MALDI
Types of MS
Ion Traps, Quads, FT-ICR, TOF, Sector

Data and Analysis

Applications
Everything is made up of Atoms
Atoms are made of protons, neutrons, and electrons
Many atoms combined together in specific
proportions to make up molecules

ATOM
Everything is made up of Atoms
Atoms are made of protons, neutrons, and electrons
Many atoms combined together in specific
proportions to make up molecules

ATOM
Molecule
Everything is made up of Atoms
Atoms are made of protons, neutrons, and electrons
Many atoms combined together in specific
proportions to make up molecules

ATOM
Molecule
Organism
Everything is made up of Atoms
Atoms are made of protons, neutrons, and electrons
Many atoms combined together in specific
proportions to make up molecules

ATOM
Molecule
Organism
6 protons (1 mass unit each) + 6 neutrons (1 mass
unit each) = 12 mass units
Electrons are negligible ( 1/3600 of mass unit)

Some carbon (about 1%) has 7 neutrons so weigh
13 units


It was found that 12 grams of carbon contains
6.02 x 10
23
atoms of carbon.

So one atom of carbon weighs 1.99 x 10
-23
grams !

12 units
Carbon Atom
1.99 x 10
-23
grams
N
N
C H
3
CH
3
N
N
CH
3
O
O
H
C
8
H
10
N
4
O
2

Total Mass = 194 Daltons(amu) = 3.22x10
-22
grams
N
N
C H
3
CH
3
N
N
CH
3
O
O
H
C
8
H
10
N
4
O
2

Total Mass = 194 Daltons(amu) = 3.22x10
-22
grams
So we must devise a machine which
can measure ~ 10
-22
grams.
Instrumental Methods Chemical Methods
Titration
Gravimetric Analysis
Solution Chemistry
Spectroscopy
Mass Spectrometry
Optical Absorption
NMR
Microwave
Optical Emission
FT-ICR
TOF
Quadrupole
Ion Trap
Linear Trap
Magnetic Sector
A technique for measuring and analyzing
molecules, that involves introducing enough
energy into a (neutral) target molecule to
cause its ionization and disintegration. The
resulting primary ions and their fragments are
then analyzed, based on their mass/ charge
ratios, to produce a "molecular fingerprint."

Mass spectrometry (Mass Spec or MS) uses
high energy electrons to break a molecule into
fragments.







Separation and analysis of the fragments
provides information about:
Molecular weight
Structure of Molecule

M
e-
e-
e-
M
(g)
+ e
-
M
+
(g)
+ 2e
-

Mass spectrometry (Mass Spec or MS) uses
high energy electrons to break a molecule into
fragments.







Separation and analysis of the fragments
provides information about:
Molecular weight
Structure of Molecule

M
e-
e-
e-
M
(g)
+ e
-
M
+
(g)
+ 2e
-

F2
Ionisation Ion Detection Ion Separation
(Mass Analyzers)
Electron Ionisation (EI)
Chemical Ionisation (CI)
Fast Atom Bombardment (FAB)
Electrospray Ionisation (ESI)
Matrix-Assisted Laserdesorption/
Ionisation (MALDI)
Quadrupole
Magnetic Sector Field
Electric Sector Field
Time-Of-Flight (TOF)
Ion Trap
Electron Multiplier
Multichannel plate
Faraday Cup
Linear Trap
In order to measure the characteristics of individual
molecules, a mass spectrometer converts them to
ions so that they can be moved about and
manipulated by external electric and magnetic
fields. The three essential functions of a mass
spectrometer, and the associated components, are:

1. The Ion Source - A small sample of compound is
ionized, usually to cations by loss of an electron
2. The Mass Analyzer - The ions are sorted and
separated according to their mass and charge
3. The Detector - The separated ions are then detected
and tallied, and the results are displayed on a chart
Solid Sample Liquid Sample Gas Sample
EI CI APCI MALDI ESI FAB
Make into Solution ? Make into Solid ? Turn into Gas?
Chemical
Properties
of analyte in
gas phase ?
Chemical
Properties
of analyte in
solution phase ?
1. Electron Impact Ionization
A beam of electrons passes through a gas-phase sample and
collides with neutral analyte molecules (M) to produce a
positively charged ion or a fragment ion. Generally
electrons with energies of 70 eV are used. This method is
applicable to all volatile compounds ( >10
3
Da) and gives
reproducible mass spectra with fragmentation to provide
structural information.

2. Chemical Impact Ionization
Ionization begins when a reagent gas (R) is ionized by
electron impact and then subsequently reacts with analyte
molecules (M) to produce analyte ions. This method gives
molecular weight information and reduced fragmentation in
comparison to EI.


3. Atmospheric-pressure chemical ionization(APCI)
Atmospheric-pressure chemical ionization (APCI) is an
ionization method used in mass spectrometry. It is a form
of chemical ionization which takes place at atmospheric
pressure.
4. Ionization by Particle Bombardment
The analyte is in a liquid matrix (with low volatility)
and is bombarded with high current of bombarding
particles. The primary particle beam is the bombarding
particle beam, while the secondary ions are the ions
produced from bombardment of the liquid target
surface.

Ionization by Particle Bombardment
5. Field Ionization (FI)
A high electric voltage (potential) that gives rise to lines of
equipotential result in an electric field crowd around the
needle tip. The electric field is most intense at the surface
(point) of the tip and is where ionization occurs.
6. Electrospray Ionization (ESI)
A solution is nebulized under atmospheric
pressure and exposed to a high electrical field
which creates a charge on the surface of the
droplet. Droplets rapidly become much smaller
through vaporization of solvent and into an
analyzer.
By producing multiply charged ions,
electrospray is extremely useful for accurate
mass measurement, particularly for thermally
labile, high molecular mass substances (ie.
proteins, oligonucleotides, synthetic polymers,
etc.)

Electrospray Ionization (ESI)
7. Matrix-Assisted Laser Desorption/Ionization
(MALDI)
Laser evaporation from a crystallized
sample/matrix mixture. The matrix material
must have an which has an absorption
spectrum that matches the laser wavelength of
energy.
Matrix acts as a receptacle for the laser energy
and facilitates ionization while minimizing
ablation of the sample and analyte ion that
would otherwise occur from direct laser
desorption.
More tolerant of salts and complex mixture
analysis than ESI.
Matrix-Assisted Laser Desorption/Ionization (MALDI)
Scanning (Filter)
Magnetic Sector
Linear Quadrupole

Pulsed (Batch)
Time-of-Flight
FT-ICR
Ion Trap

( Separation in Space)
( Separation in Time)
ma F =
zE F =
zV mv E K = =
2
2
1
. .
m mass
a acceleration
B Magnetic Field
z elementary charge(z=q/e)
E - electric field
F Force
K.E. kinetic energy
V electric potential
v - velocity
zvB F =
zE ma =
m
zE
a

=
m
zE
a

=
We can
control this.
(volts/meter)
We can
measure
this.
m
zE
a

=
We can
control this.
(volts/meter)
We can
measure
this.
We can deduce This !
Mass analyzers separate the ions according to their mass-to-charge ratio.
The following two laws govern the dynamics of charged particles in
electric and magnetic fields in vacuum:
(Lorentz force law);

(Newton's second law of motion in
non-relativistic case, i.e. valid only at ion
velocity much lower than the speed of light).

Here F is the force applied to the ion, m is the mass of the ion, a is the
acceleration, z is the elementary charge, E is the electric field,
and v B is the vector cross product of the ion velocity and the magnetic
field.
Equating the above expressions for the force applied to the ion yields:




) ( B v E z F + =
ma F =
B v E a
z
m
+ =
|
.
|

\
|
The most common data representation is the mass
spectrum.

Certain types of mass spectrometry data are best
represented as a mass chromatogram.

Other types of mass spectrometry data are well
represented as a three-dimensional contour map.
In this form, the mass-to-charge, m/z is on the x-
axis, intensity the y-axis, and an additional
experimental parameter, such as time, is recorded
on the z-axis.

Isotope ratio MS: isotope dating and tracking

Trace gas analysis

Atom probe (location of individual atoms)

Pharmacokinetics (testing blood or urine samples)

Protein characterization (characterization and sequencing of
proteins)

Glycan analysis( polysaccharide, oligosaccharide, glycoprotein,
glycolipid, proteoglycan)

Space exploration (Exploration of Atmosphere, Water and
Hydrocarbons on different planets)

Respired gas monitor (Anesthesia, Spirometry)