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Mussarat Jabeen
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Mussarat Jabeen
• Powerful analytical technique
• Smallest scale
• Destructive technique
• Useful for identification of species
Mass spectrometer
Joseph John Francis William Wolfgang Paul John Bennet Koichi Tanaka
Thomson Aston 1989 Nobel Prize for Fenn 2002 Nobel Prize
1906 Nobel Prize for 1922 Nobel Prize for Physics 2002 Nobel Prize for Chemistry
Physics Chemistry (for the development for Chemistry (mass
(theoretical and (mass spectrograph, of the ion trap (for the spectrometric
experimental of isotopes, in a technique) development of analyses of
investigations on the large number of non- Soft Desorption biological
conduction of radioactive ionization Method) macromolecules)
electricity by gases) elements)
Mass spectrometer
Understanding Mass Spectrometry
Two techniques
Commonly used
•Protonation
•Deprotonation
•Cationization
•Transfer of a charged molecule to the gas phase
•Electron ejection
•Electron capture
Protonation
where the spray needle has been made very small and
is positioned close to the entrance to the mass analyzer.
The end result of this rather simple adjustment is
increased efficiency, which includes a reduction in the
amount of sample needed.
•Very sensitive
•very low flow rates
•Very small droplet size (~5µ)
Atmospheric Pressure Chemical Ionization (APCI)
the liquid effluent of APCI is introduced directly into the ionization source.
However, the similarity stops there. The droplets are not charged and the
APCI source contains a heated vaporizer, which facilitates rapid
desolvation/vaporization of the droplets. Vaporized sample molecules are
carried through an ion-molecule reaction region at atmospheric pressure.
Atmospheric pressure photoionization (APPI)
the analyte is first co-crystallized with a large molar excess of a matrix compound, usually a UV-
absorbing weak organic acid. Irradiation of this analyte-matrix mixture by a laser results in the
vaporization of the matrix, which carries the analyte with it. The matrix plays a key role in this
technique. The co-crystallized sample molecules also vaporize, but without having to directly
absorb energy from the laser. Molecules sensitive to the laser light are therefore protected from
direct UV laser excitation.
Fast Atom Bombardment (FAB)
Immobilized matrix is bombarded with a fast
beam of Argon or Xenon atoms. Charged
sample ions are ejected from the matrix and
extracted into the mass
analyzers
possible mechanism
Reagent (R) + e- → R+ + 2 e-
R+ + RH → RH+ + R
RH+ + Analyte (A) → AH+ + R
used to
•quantify toxic trace elements in foods.
•measurement of stable isotope ratio of
inorganic elements.
Mass Analyzer
Properties of mass Analyzer
•Quadrupoles
•Quadrupole Ion Trap
•Linear Ion Trap
•Double-Focusing Magnetic Sector
•Quadrupole Time-of-Flight Tandem MS
•Quadrupole Time-of-Flight MS
Quadrupoles
-ions travel parallel to four rods
- opposite pairs of rods have
rapidly alternating potentials
(AC)
- ions try to follow alternating
field in helical trajectories
- stable path only for one m/z
value for each field frequency
The quadrupole ion trap typically consists of a ring electrode and two hyperbolic endcap
electrodes. The motion of the ions induced by the electric field on these electrodes allows ions
to be trapped or ejected from the ion trap. In the normal mode, the radio frequency is scanned
to resonantly excite and therefore eject ions through small holes in the endcap to a detector. As
the RF is scanned to higher frequencies, higher m/z ions are excited, ejected, and detected.
Linear Ion Trap
The linear ion trap differs from the 3D ion trap as it confines ions along the axis of a
quadrupole mass analyzer using a two-dimensional (2D) radio frequency (RF) field
with potentials applied to end electrodes. The primary advantage to the linear trap
over the 3D trap is the larger analyzer volume lends itself to a greater dynamic ranges
and an improved range of quantitative analysis.
Double-Focusing Magnetic Sector
the ions are accelerated into a magnetic field using an electric field. A charged particle
traveling through a magnetic field will travel in a circular motion with a radius that depends on
the speed of the ion, the magnetic field strength, and the ion’s m/z. A mass spectrum is
obtained by scanning the magnetic field and monitoring ions as they strike a fixed point
detector.
Quadrupole Time-of-Flight Tandem MS
Faraday Cup
Array Detector
Electron Multiplier
Faraday Cup
A Faraday cup involves an ion striking
the dynode (BeO, GaP, or CsSb)
surface which causes secondary
electrons to be ejected. This temporary
electron emission induces a positive
charge on the detector and therefore a
current of electrons flowing toward the
detector.
is not as commonly
Life limit is high as compared to others.
Array Detector
detects ions according to their different m/z, has
been typically used on magnetic sector mass
analyzers.
Fragmentation peaks
The peaks observed by fragments of
compounds.
Stevenson’s Rule
Homolytic bond cleavage
Heterolytic fragmentation
Alpha cleavage
Beta-cleavage
Inductive cleavage
Retro Diels-Alder Cleavage
McLafferty rearrangement
Ortho effect
Onimum Reaction
CO Elimination
Stevenson’s Rule
The most probable fragmentation is the one that leaves
the positive charge on the fragment with the lowest
ionization energy
In other words, fragmentation processes that lead to the
formation of more stable ions are favored over
processes that lead to less-stable ions.
•DBR Calculations
•Nitrogen Rule
•Isotopic effect
DBR Calculations
Double bond or ring calculations tell us about how many rings or double
bonds are present in a compound.
DBR= C-H/2+N/2+1
C= number of carbon atoms
H= number of hydrogen atoms
N= number of nitogen atoms
Nitrogen Rule
•If a compound contains an even number of nitrogen atoms (or no
nitrogen atoms), its molecular ion will appear at an even mass number.
• If, however, a compound contains an odd number of nitrogen
atoms, then its molecular ion will appear at an odd mass value.
• This rule is very useful for determining the nitrogen content of an
unknown compound.
Isotopic effect
Mass spectra (examples)
Alkanes
Strong M+ (but intensity decreases with an increase of branches.
Carbon-carbon bond cleavage
loss of CH units in series: M-14, M-28, M-42 etc
Alkanes
Cycloalkanes
Strong M+, strong base peak at M-28 (loss of ethene)
A series of peaks: M-15, M-28, M-43 etc
Methyl, ethyl, propyl with an additional hydrogen give peaks
Alkenes Strong M+
Fragmentation ion has formula CnH2n+ and CnH2n-1
-Cleavage
A series of peaks: M-15, M-29, M-43, M-57 etc
Alkynes
Strong M+
Strong base peak at M-1 peak due to the loss of terminal hydrogen
Alpha cleavage
Aromatic Hydrocarbons
Strong M+
Loss of hydrogen gives base peak
McLafferty rearrangement
Formation of benzyl cation or tropylium ion
Alcohols
M+ weak or absent
Loss of alkyl group via a-cleavage
Dehydration (loss of water) gives peak at M-18
Phenols
Strong M+
M-1 due to hydrogen elimination
M-28 due to loss of CO
M-29 due to loss of HCO (formyl radical)
Ethers
M+ weak but observable
Loss of alkyl radical due to a-cleavage
B-cleavage( formation of carbocation fragments through loss of alkoxy radicals)
C-O bond cleavage next to double bond
Peaks at M-31, M-45, M-59 etc
Aldehyde M+ weak, but observable (aliphatic)
Aliphatic : M-29, M-43 etc
McLafferty rearrangement is common gives the base peak
A-cleavage
B-cleavage
Aldehyde
M+ strong (aromatic)
Aromatic: M-1 (loss of hydrogen)
M-29 (loss of HCO)
McLafferty rearrangement is common
A-cleavage
B-cleavage
Ketones
Strong M+
A series of peaks M-15, M-29, M-43 etc
Loss of alkyl group attached to the carbonyl group by a-cleavage
Formation of acylium ion (RCO+)
McLafferty rearrangement
Esters
M+ weak but generally observable
Loss of alkyl group attached to the carbonyl group by a-cleavage
Formation of acylium ion (RCO+)
McLafferty rearrangement
Acyl portion of ester OR+
Methyl esters: M-31 due to loss of OCH3
Higher esters: M-32, M-45, M-46, M-59, M-60, M-73 etc
Carboxylic acids
Aliphatic carboxylic acids:
M+ weak but observable
A-cleavage on either side of C=O
M-17 due to loss of OH
M-45 due to loss of COOH
McLafferty rearrangement gives base peak
Aromatic carboxylic acids:
M+ Strong
A-cleavage on either side of C=O
M-17 due to loss of OH
M-18 due to loss of HOH
M-45 due to loss of COOH
McLafferty rearrangement gives base peak
Amines
M+ weak or absent
Nitrogen rule obey
A-cleavage
Nitriles
M+ seldom observed
Loss of NO+ give visible peak
Loss of NO2+ give peak
Alkyl chloride and alkyl bromides
Strong M+2 peak
For Cl M/M+2 = 3:1
F or Br M/M+2 = 1:1
A-cleavage
Loss of Cl or Br
Loss of HCl or HBr
Alkyl chloride
Applications of Mass Spectrometry
The technique has both quantitative and qualitative
uses. These include identifying unknown compounds,
determining the isotopic composition of elements in a
molecule, and determining the structure of a
compound by observing its fragmentation. Followings
are the main applications
Toxicity of Toothpastes
Measuring nanoparticle size
Pharmacokinetics
Protein characterization
Space exploration
Isotope dating and tracking
Molecular weight
Bonding
Reaction mechanism
Toxicity of Toothpastes
DEG (diethylene glycol) which is a toxic chemical and usually present in
Chinese toothpastes.
Space exploration
Mass spectrometers are also widely used in space missions to measure the
composition of plasmas. For example, the Cassini spacecraft carries the
Cassini Plasma Spectrometer (CAPS),[44] which measures the mass of ions
in Saturn's magnetosphere.
Bonding
Bonding can be studied by fragmentation patterns for example, beta
cleavage is possible only if double bonds or heteroatom present.
Reaction mechanism
Mass spectrometry is best technique to study reaction mechanism and
intermediates produced in reaction, for example, in carboxylic acid and
alcohols a peak at M-18 indicates that water is produced.
Determination of Elements
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