Mass Spectrometry
Dr Richard W. McCabe
M57
rwmccabe@uclan.ac.uk
1
Mass Spectrometry
In Mass Spectrometry the sample is introduced into
a high vacuum chamber and ionised, by a variety of
methods, but most commonly by electron impact to
give high energy positive ions that break up
 The mixture of ions are attracted to an electrode with
a hole that allows a “spray” of ions to enter the
analyser
 The analyser separates the ions by applying
electrical and/or magnetic fields to separate the ions
in terms of their mass to charge ratios

2
Ionisation



Mass spectrometry is the analysis of, usually, +ve ions
generated, for example, either by removal of an electron
from a molecule (Electron Impact, EI) or by acquisition of
a +ve charge by Fast Atom Bombardment (FAB) or by
impact with a +ve ion (Chemical Ionisation, CI), etc.
The +ve molecular ions acquire sufficient extra energy in
the process that they fragment into smaller “daughter”
ions. N.B. Very high vacuum is maintained to promote
unimolecular reactions and minimise bimolecular ones.
These +ve ions are separated by combinations of magnetic
and/or electrical fields and are detected as ion currents
which are then displayed via a computer as:
m/z vs. % Abundance
3
Electron Impact Ionisation, EI

The molecules in the vapour phase collide with a high
energy (usually ca. 70eV) electron beam. The
electrons “knock out” an electron from an orbital of
the molecule and also leave the radical cation in a
high energy state. The molecular ion then fragments.
M + e -*
M 1+ +
M + . * + 2e -
R 1.
M 2+ +
R 2.
M 3+ +
N3
4
Fast Atom Bombardment - FABms

Sometimes when the sample is not very volatile the
compound can be dissolved in a low volatility solvent (e.g.
glycerol) and bombarded with fast atoms, usually xenon.
The fast xenon atoms are generated by accelerating xenon
cations (made by EI) and passing them through xenon gas.
X e+ + X e
X e + X e+
M + .* + M H + + e -
M + Xe
M 4+ +
M 1+ +
R 1.
M 2+ +
R 2.
M 3+ +
N4
N3
5
Chemical Ionisation, CI

If a gas is let into the EI chamber it will ionise. If the
pressure of the gas is high enough then collisions occur
which may result in protonation of the ionised gas. The
protonated gas can then be used to impact the sample and
ionise the molecules by transferring a H+ to the molecule.
C H 4 + e-
C H 4 + .* + e C H 5+* + C H 3.
C H 4 + .* + C H 4
C H 5+* + M
M 1+ +
M H +* + C H 4
R 1.
M 2+ +
R 2.
iso-Butane and ammonia
are also used but they give
weaker acids.
M 3+ +
N3
6
Gas Chromatography/ Mass Spectrometry



The components in a volatile mixture can be separated by
gc and a portion of the effluent gasses passed into the
ionisation chamber of a mass spectrometer and separated.
A mass spectrum can be obtained ca. every second and a
chromatogram of the total ion current vs. time obtained.
As each point on the chromatogram is associated with a
full mass spectrum a computer is needed to store the data.
As the pressure in gc/ms is relatively high, bimolecular
collisions are relatively frequent. Thus even with EI
ionisation, spectra often have some characteristics of CI
spectra (i.e. MH+), especially when a basic N is present.
7
Fragmentation of Butane, C4H10 = 58
8
Fragmentation of Butane, C4H10
M ass
59
A ssignm ent
58
C 4H 10
+
M
+
C 3H 7
43
+
13
C C 3H 10
+
= M + 1
+
=
“N eutral”
n/a
R eaction /C om m ent
n/a
M + e  M
CH3
13
C isotope peak  4 x 1.1% of 58
-

+
+ 2e
+
-
.
+ CH3
+
41
C 3H 5
+
H2
+
+
+
H2
+
H2
.
P roduct (41) resonance stabilised
39
29
27
15
C 3H 3
+
C 2H 5
+
C 2H 3
CH3
+
+
H2
C 2H 5

H2
C 3H 7
+
+
P roduct (39 ) resonance stabilised
+ .
+
+

+
+
+ C 2H 5
.
+ H2
.
CH3
+
+
.
9
Fragmentation of Methylpropane, C4H10 = 58
10
Fragmentation of methylpropane
M ass
59
A ssignm ent
58
C 4H 10
+
M
+
C 4H 9
57
43
+
13
C C 3H 10
+
= M + 1
C 3H 7
+
+
=
“N eutral”
n/a
R eaction/C om m ent
n/a
M + e  M + 2e
N ote: this peak is m uch sm aller than w ith butane
H
13
C isotope peak  4 x 1.1% of 58
+
-

CH3
H

-
.
+
+
+
C 3H 5
+
H2
H
+
.
CH3
.
+
41
.
+
+
+
+
H2
+
H2
P roduct (41) resonance stabilised
39
C 3H 3
+
29
C 2H 5
+
H2
+
+
P roduct (39) resonance stabilised
C 2H 5

R earrange
+
27
15
C 2H 3
CH3
+
+
H2
C 3H 7
+
+
.
+
+

+
.
+ C 2H 5
.
+ H2
.
.
CH3
+
+
11
Isotopes – Chloroethane = 64 & 66
12
Fragmentation of chloroethane
“N eutral”
n/a
R eaction/C om m ent
+
=
n/a
M + e  M + 2e
N ote: peak s 64 and 66 are in the ratio of 3:1
=
n/a
M + e  M
M ass
67
A ssignm ent
66
C 2H 5 C l
+
M
64
C 2H 5 C l
+
M
37
+
C lC H 2
51
49
29
28
13
37
CCH5 Cl
+
= M + 1
35
37
+
35
+
C lC H 2
C 2H 5
C 2H 4
+
+
+
CH3
CH3
Cl
13
C isotope peak  2 x 1.1% of 66
-
+
-
+

37

+ 2e
+
Cl
-
.
+
37
Cl
+
Cl
.
+
+
Cl
26
C 2H 3
C 2H 2
+
+
H2
H2
+
+
+
.
+
Cl
.
.
H
27
.
CH3
+
N ote: peak s 51 an d 49 are in the ratio of 3:1
+ .
35
+
.
Cl
+ CH3
35
Cl

HCl
-
+
+
.
+
H -C l
+ H2
.
+
H2
13
Isotopes 2 – 1-Bromopropane = 122 & 124
14
Fragmentation of 1-bromopropane
M ass
124
A ssignm ent
122
C 3H 7 B r
+
= M
82
H Br
81
+
79
+
C 3H 7 B r
+
= M
81
+
“N eutral”
n/a
R eaction/C om m ent
n/a
M + e  M
-
+
-
+
-
M + e  M + 2e
N ote: peaks 122 and 124 are in the ratio 1:1
+ 2e
C 3H 6
81
+
-
.
.
+ H -8 1B r +
Br
H
81
81
Br
+
C 3H 7
N ote: peaks 80 and 82 are in the ratio 1:1
+ .
81
. +
Br

81
B r+
N ote: peaks 79 and 81 are in the ratio 1:1
80
81
H Br
+
C 3H 6
79
+
.
+
.
+ H - 7 9 B r+
Br
H
79
29
79
Br
+
C 2H 5
27
C 2H 3
15
+
CH3
C 3H 7
+
+
C 2H 5

79

Br
H2
B rC 2 H 5
. +
Br
+
.
+
+
+

Br
+
79
+ B rC H 2
.
B r+
.
+ H2
.
CH3
+
+ Br
.
15
Aromatic rings are stable – Toluene = 92
16
Fragmentation of toluene
M ass
93
A ssignm ent
92
C 7H 8 =
+
M
+
C 7H 7
91
13
C C 6H 8
+
= M
+
+
“N eutral”
n/a
R eaction/C om m ent
n/a
M + e  M
H
13
C isotope peak  7 x 1.1% of 92
-
+

+
H
+
C 2H 2
+
C 3H 3
C 4H 4
65
C 5H 5
51
39
C 4H 4
+
C 3H 3
+ 2e
-
.
+
.
+
H
N ote: peaks 92 highly stabilised by resonance
N ote: peaks 65, 51 and 39 are fragm ents of the ring
in 91
17
Functional Groups – ethanol = 46
18
Fragmentation of ethanol
M ass
46
45
A ssignm ent
+
C 2H 6O =
+
M + 1
+
C 2H 5O
“N eutral”
n/a
H

R eaction/C om m ent
-
M + e  M
+
+ 2e
-
H
+
H
.
OH
43
C 2H 3O
+
H2
+
C
+
CH3

+
.
C 3H 3
+
H2
H
C 2H 5
+
HO

H
+
19
15
C 2H 3
+
H2
.
+
.
+
+
+ CH3
OH
+
OH
27
CH3
H
.
OH
29
+
HO
+
H2
+
OH
30
+
O
O
+
C H 3O
.
H
H
31
+ H
OH
+
+
HO
.
.
+ H2
+
H 3O
+
CH3
C H 3O

+
OH
.
CH3
.
+
+
OH
19
Propanone (acetone) = 58
20
Fragmentation of propanone
M ass
59
A ssignm ent
58
C 3H 6O =
+
M
+
C 2H 3O
43
13
C C 2H 6 O
+
= M + 1
+
+
“N eutral”
n/a
R eaction/C om m ent
n/a
M + e  M
CH3
13
C isotope peak  3 x 1.1% of 58
-
+
+ 2e
-

+
.
+
C
O
O
29
27
15
+
C 2H 5
+
C 2H 3
CH3
+
+
CH3
.
N ote: can only be form ed b y a rearrangem ent
H2
C 2H 3O
or C O
+
+
+ H2

+
.
.
O
O
+
C H 3+
+
and
C
O
CO
+
C H 3+
21