Mass Spec

Mass
Spectrometry (MS)
Introduction
 Mass spectrometry (MS) is an analytical method
of characterizing matter, based on the
determination of atomic or molecular masses of
individual species presentin a sample.
 Mass spectrometry (Mass Spec or MS) is one of
the techniques used for deriving structure of a
molecule
Other techniques –NMR
-IR
 MS uses high energy electrons to break a

molecule into fragments.
Introduction…
 Separation and analysis of the fragments
provides information about:
 Molecular weight
 Structure
 Most important b/c it tells the mass of

the molecule—easy to know the atoms of
the molecule
Basic principles
 A minute quantity of sample, transformed
in the gas phase or in a suitable form, is
ionized
 The resulting charged species are then

submitted, in an enclosed space maintained
under high vacuum, to the action of an
electric and/or magnetic field, depending
on the type of instrument.
Basic principles…
 The study of the forces exerted upon
the ions allows the determination of their
mass-to-charge ratio and, eventually
their nature.
 This method destroys the compound

sample, but owing to the great sensitivity
of the technique, only a tiny quantity is
required.
Basic principles…
1. Ionization
 The impact of a stream of high energy
electrons causes the molecule to lose an
electron forming a radical cation.
 A species with a positive charge and
one unpaired electron
M + e- → M●+ + 2e-
H H
- -
H C H + e H C H + 2e
H H
Molecular ion (M+)
m/z = 16
Basic principles…
 The formed radical cation is highly unstable–
it is again broken into fragments.
H H
+
H C C H molecular ion (M ) m/z = 30
H H
H H H H
-
H C C H + e + H
H C C
H H H H
m/z = 29
H H
m/z = 15 H C + C H (not detected by MS)
H H
Basic principles…
 Molecular ion (parent ion):
 The radical cation corresponding to the
mass of the original molecule
H H H
H C H H C C H
H H H
 The molecular ion is usually the highest
mass in the spectrum
 Some exceptions with specific isotopes
 Some molecular ion peaks are absent.
Basic principles…
 Mass spectrum of ethanol (MW = 46)
M+
Basic principles…
2. Acceleration
 Once formed, the ions are immediately

extracted from this part of the
instrument to be focussed and
accelerated by a series of electronic
lenses, to increase their kinetic energy.
Basic principles…
3. Separation
 The ions are then ‘filtered’ by the

analyser according to their mass-to-
charge ratio
 A number of instruments combine several

mass analysers in series.
Basic principles…
4. Detection
 After separation, ions terminate their flight

by striking the sensor of the detector which
measures electrical charge and amplifies the
weak ionic current.
Basic principles…
5. Display of the mass spectrum arising
from treatment of the signal sent by the
detector.
Instrumentation of Mass Spec
Instrumentation…
Major components are
 Sampling port
 Heating chamber
 Electron gun
 Electron collector
 Magnetic field region
 Detector
Instrumentation…
 The larger the mass of the fragment the
lower it will be deflected.
 Large molecules will be detected first

then intermediate then the smaller ones
 By changing the strength of the magnetic

field we can manage the detection of
each fragment
Plotting and analyzing the mass spectrum
 The resulting mass spectrum is a graph of

the mass of each cation vs. its relative
abundance (intensity).
 The peaks are assigned an abundance as a

percentage of the base peak.
 The base peak is the most intense peak in
the spectrum
 The base peak is not necessarily the same

as the parent ion peak.
The mass spectrum of ethanol
base peak
M+
Easily Recognized Elements in MS
 Nitrogen:
Nitrogen rule: In general, “small” organic molecules with an odd mass must have an odd number of nitrogens.
Organic molecules with an even mass have zero or an even number of nitrogens.
 Odd number of N = odd MW
+
M = 41
CH3CN
Easily Recognized Elements in MS…
 Bromine:
 M+ ~ M+2 (50.5% 79Br/49.5% 81Br)
2-bromopropane
M+ ~ M+2
 Chlorine:
 M+2 is ~ 1/3 as large as M+
Cl M+
M+2
 Iodine
 I+ at 127 Large gap M+
 Large gap
ICH2CN I+
Fragmentation Patterns
 The impact of the stream of high energy

electrons often breaks the molecule into
fragments, commonly a cation and a radical.
 Bonds break to give the most stable

cation.
 Stability of the radical is less important.
Fragmentation Patterns…
Alkanes
 Fragmentation often splits off simple

alkyl groups:
 Loss of methyl M+ - 15
 Loss of ethyl M+ - 29
 Loss of propyl M+ - 43
 Loss of butyl M+ - 57
 Branched alkanes tend to fragment

forming the most stable carbocations.
Mass spectrum of 2-methylpentane
Alkenes:
Fragmentation typically forms resonance
stabilized allylic carbocations
Aromatics:
Fragment at the benzylic carbon, forming a resonance
stabilized benzylic carbocation (which rearranges to the
tropylium ion)
H H H
H C Br H C H C
or
M+
Aromatics may also have a peak at m/z = 77 for the
benzene ring.
77
NO2
M+ = 123
77
Alcohols
 Fragment easily resulting in very small or

missing parent ion peak
 May lose hydroxyl radical or water
 M+ - 17 or M+ - 18
 Commonly lose an alkyl group attached to the

carbinol carbon forming an oxonium ion.
 1o alcohol usually has prominent peak at
m/z = 31 corresponding to H2C=OH+
 Ethers
 -cleavage forming oxonium ion
 Loss of alkyl group forming oxonium ion
 Loss of alkyl group forming a

carbocation
MS of diethylether (CH3CH2OCH2CH3)
H O CH2 CH3CH2O CH2
H O CHCH3
 Aldehydes (RCHO)
 Fragmentation may form acylium ion
RC O
 Common fragments:
 M+ - 1 for RC O
 M+ - 29 for R (i.e. RCHO - CHO)

 MS for hydrocinnamaldehyde
105 91
H H O
C C C H
M+ = 134
H H
133 105
91
O
 Ketones RCR'
 Fragmentation leads to formation of
acylium ion:
 Loss of R forming R'C O
 Loss of R’ forming RC O
Fragmentation Patterns… O
CH3CCH2CH2CH3
 MS for 2-pentanone
CH3C O
CH3CH2CH2C O
M+
SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of

Advanced Industrial Science and Technology, 11/28/09)
Rule of Thirteen
 The “Rule of Thirteen” can be used to
identify possible molecular formulas for an
unknown hydrocarbon, CnHm.
 Step 1: n = M+/13 (integer only, use

remainder in step 2)
 Step 2: m = n + remainder from step 1

Rule of Thirteen…
 Example: The formula for a hydrocarbon
with M+ =106 can be found:
 Step 1: n = 106/13 = 8 (R = 2)
 Step 2: m = 8 + 2 = 10
 Formula: C8H10
Rule of Thirteen…
 If a heteroatom is present,
 Subtract the mass of each heteroatom
from the MW
 Calculate the formula for the
corresponding hydrocarbon
 Add the heteroatoms to the formula
Rule of Thirteen…
Example: A compound with a molecular ion
peak at m/z = 102 has a strong peak at
1739 cm-1 in its IR spectrum. Determine
its molecular formula.
Applications in mass spectrometry
1. Identification by means of a spectral library
2. Analysis of the elementary composition of ions
(molecular formula determination)
3. Determination of molecular masses from
multicharged ions
4. Determination of isotope ratios for an
element
5. Identification of organic ions by looking at
fragmentation patterns
6. Integration with GC and HPLC (GC-MS,
HPLC-MS)
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Mass Spec

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Mass

 MS uses high energy electrons to break a

 Most important b/c it tells the mass of

 The resulting charged species are then

 This method destroys the compound

 Once formed, the ions are immediately

 The ions are then ‘filtered’ by the

 A number of instruments combine several

 After separation, ions terminate their flight

 Large molecules will be detected first

 By changing the strength of the magnetic

 The resulting mass spectrum is a graph of

 The peaks are assigned an abundance as a

 The base peak is not necessarily the same

 The impact of the stream of high energy

 Bonds break to give the most stable

 Fragmentation often splits off simple

 Branched alkanes tend to fragment

 Fragment easily resulting in very small or

 Commonly lose an alkyl group attached to the

 Loss of alkyl group forming oxonium ion

 Loss of alkyl group forming a

H O CH2 CH3CH2O CH2

 M+ - 29 for R (i.e. RCHO - CHO)

 Loss of R forming R'C O

SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of

 Step 1: n = M+/13 (integer only, use

 Step 2: m = n + remainder from step 1

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