Saturn GC/MS

MASS SPECTRAL INTERPRETATION

QUICK
REFERENCE
GUIDE

03-914351-00:R2

GRAPHICAL REPRESENTATION OF
RELATIVE ISOTOPE PEAK INTENSITIES FOR
ANY GIVEN ION CONTAINING THE INDICATED
NUMBER OF HALOGENS

CHLORINE-BROMINE ISOTOPE ABUNDANCE

RATIOS
Cl-Br

X+2

X+4

X+6

X+8

X+10

Cl

100

32.5

Cl2

100

65.0

10.6

Cl3

100

97.5

31.7

3.4

Cl4

76.9

100

48.7

10.5

0.9

Cl5

61.5

100

65.0

21.1

3.4

0.2

Cl6

51.2

100

81.2

35.2

8.5

1.1

ClBr

76.6

100

24.4

Cl2Br

61.4

100

45.6

6.6

Cl3Br

51.2

100

65.0

17.6

ClBr2

43.8

100

69.9

13.7

Cl2Br2

38.3

100

89.7

31.9

3.9

Cl3Br2

31.3

92.0

100

49.9

11.6

ClBr3

26.1

85.1

100

48.9

8.0

Cl2Br3

20.4

73.3

100

63.8

18.7

Br

100

98.0

Br2

51.0

100

49.0

Br3

34.0

100

98.0

32.0

Br4

17.4

68.0

100

65.3

1.7

16.0

1.0

2.0

EXACT MASSES AND NATURAL ISOTOPIC

ABUNDANCE RATIOS
Element

Symbol

Intg.
Mass

Exact
Mass

Abundance

X+1
Factor*

X+2
Factor*

Hydrogen

H
D or 2H

1
2

1.0078
2.0141

99.99
0.01

12C

12
13

12.0000
13.0034

98.91
1.1

1.1nC

0.0060nC2

14N

14
15

14.0031
15.0001

99.6
0.4

0.37nN

18O

16
17
18

15.9949
16.9991
17.9992

99.76
0.04
0.20

Fluorine

19

18.9984

100

Silicon

28Si
30Si

28
29
30

27.9769
28.9765
29.9738

92.2
4.7
3.1

Phosphorus

31

30.9738

100

Sulphur

32S

32
33
34

31.9721
32.9715
33.9679

95.02
0.76
4.22

Carbon

Nitrogen

13C

15N

Oxygen

16O
17O

29Si

33S
34S

0.04nO
0.20nO

5.1nSi
3.4nSi

0.8nS
4.4nS

Chlorine

35Cl

35
37

34.9689
36.9659

75.77
24.23

32.5nCl

Bromine

79Br

79
81

78.9183
80.9163

50.5
49.5

98.0nBr

Iodine

127

126.9045

100

1.
2.
3.

37Cl

81Br

The integer mass of the most abundant naturally-occurring

stable isotope is the nominal mass of the element.
The exact mass of the most abundant naturally occurring
stable isotope is the mono-isotopic mass of the element.
The atomic weight is the average mass of the element.

*Assume X = 100%; X represents the relative intensity of the first

peak in a cluster of peaks corresponding to isotopic variants of a
given ion.
The factor is multiplied by the number (n) of atoms of the element
present to determine the magnitude of the intensity contribution for
a given isotope. For example, the contribution at X+1 due to 15N
for an ion containing three nitrogens would be 0.37 x 3 = 1.11
relative to 100 at X.

ISOTOPIC CONTRIBUTIONS FOR C AND H

C#

(X+1)+

(X+2)+

C#

(X+1)+

(X+2)+

C1
C2
C3
C4
C5
C6
C7
C8
C9
C10
C11
C12
C13
C14
C15
C16
C17
C18
C19
C20

1.1
2.2
3.3
4.4
5.5
6.6
7.7
8.8
9.9
11.0
12.1
13.2
14.3
15.4
16.5
17.6
18.7
19.8
20.9
22.0

0.01
0.02
0.05
0.10
0.15
0.22
0.29
0.38
0.49
0.60
0.73
0.86
1.0
1.2
1.3
1.5
1.7
1.9
2.2
2.4

C21
C22
C23
C24
C25
C26
C27
C28
C29
C30
C31
C32
C33
C34
C35
C36
C37
C38
C39
C40

23.1
24.2
25.3
26.4
27.5
28.6
29.7
30.8
31.9
33.0
34.1
35.2
36.3
37.4
38.5
39.6
40.7
41.8
42.9
44.0

2.6
2.9
3.2
3.4
3.7
4.1
4.4
4.7
5.0
5.4
5.8
6.1
6.5
6.9
7.3
7.8
8.2
8.7
9.1
9.6

The isotopic contributions for other elements is additive.

UNREASONABLE SUGGESTED LOSS FROM

THE MOLECULAR ION
M7
M3
M6
These do not correspond to the mass of groups of atoms likely
to be lost from most common organic molecules; they probably
result from noise spikes or ions from an impurity.
As a general rule, 3 to 14 and 21 to 26 is not a reasonable loss.

TYPES OF POSITIVE-ION CI REACTIONS

Gas-phase analytes can undergo four different types of

reactions with the reagent ions in positive-ion CI. It should be
noted that only charge transfer results in the formation of an
OE+. ion. All the other reaction mechanisms result in the
formation of EE+ ions.
CHARGE TRANSFER

CH4+. +

RH RH+.

CH4 (M+.)

PROTON TRANSFER

CH5+ +
C2H5+ +

RH RH2+ +
RH RH2+ +

CH4 (M + 1)+
C2H4

HYDRIDE ABSTRACTION

CF3+

RH R+

CF3H (M 1)+

COLLISION-STABILIZED COMPLEXES

C2H5+ +

RH (C2H5:RH)+

(M + 29)+

C3H5+ + RH (C3H5:RH)+
(M + 41)+
Acetonitrile and methanol along with other reagents that exist
as a liquid under normal pressure and temperatures, can be
used easily in the internal ionization ion-trap mass
spectrometer.
Reagent

Reagent Ion

Proton Affinity
(kcal mol-1)

CH4
H2O
CH3OH
C2H5OH
CH3CN
iC4H10
NH3
CH3NH2

CH5+
H3O+
CH3OH2+
C2H5OH2+
CH3CNH+
iC4H9+
NH4+
CH3NH3+

132
167
182
186
188
196
204
211

STEPS IN THE INTERPRETATION OF A MASS

SPECTRUM
1. Note general appearance of spectrum to see if it is
interpretable.
2. Select a candidate peak for the molecular ion (M+. ).
3. Examine spectrum for peak clusters of characteristic
isotopic patterns.
4. Test M+. candidate by searching for peaks corresponding to
reasonable loss.
5. Look for characteristic low-mass fragment ions.
6. Compare spectrum to reference spectra:
a. Using compilations in published references
b. Using computerized search of reference spectra
7. Spectral interpretation must be reconciled with all other
information about the sample.
8. Check interpretation by obtaining spectrum of putative
compound under some instrumental conditions.

CRITERIA FOR RECOGNIZING AND PROVING

VALIDITY OF MOLECULAR ION
1. If compound is known, molecular ion will have an m/z value
equal to the sum of the atomic masses of the most
abundant isotope of each element that comprises the
molecule.
2. The M+. peak must be the highest m/z value peak of
significance (non-background, non isotope).
3. The nominal molecular weight or m/z value for the
molecular ion will be an even number for any compound
containing only C, H, O, S, Si, P and halogens.

Fragment ions derived via homolytic fission from

these ions will have an odd m/z value.

Fragment ions derived from these molecular ions

(even mass) via expulsion of neutral components
(e.g., H2O, CO, ethylene, etc.) will themselves have
an even value of m/z.
4. Nitrogen Rule: A compound containing an odd number of
nitrogen atoms in addition to C, H, O, S, Si, P and
halogens will have an odd molecular weight.
5. No fragment ion may contain a larger number of atoms of
any particular element than the M+..

McLAFFERTY REARRANGEMENT

FORMATION OF TROPYLIUM ION

RINGS PLUS DOUBLE BONDS

For a proposed molecular formula, the
rings plus double bonds can be
calculated by adding the number of
carbons plus 1 to the number of
nitrogens divided by 2, and subtracting
the number of hydrogens divided by 2.
If the value ends in 1/2, round down to
obtain the applicable value.

SOME COMMON AND REASONABLE LOSSES

FROM THE MOLECULAR ION
M-1
M - 15
M - 29
M - 31
M - 43
M - 45
M - 57
M-2
M - 18
M - 28
M - 32
M - 44
M - 60
M - 90

loss of hydrogen radical

loss of methyl radical
loss of ethyl radical
loss of methoxyl radical
loss of propyl radical
loss of ethoxyl radical
loss of butyl radical
loss of hydrogen
loss of water
loss of CO or ethylene
loss of methanol
loss of CO2
loss of acetic acid
loss of silanol: HO-Si(CH3)3

M-H

M - CH3

M - CH2CH3

M - OCH3

M - CH2CH2CH3

M - OCH2CH3

M - CH2CH2CH2CH3
M - H2
M - H2O
M - CO or M- C2H4
M - CH3OH
M - CO2
M - CH3CO2H
M - HO-Si(CH3)3

NEUTRAL FRAGMENTS EXPELLED BY

SIMPLE CLEAVAGE

Mass
1

15
16
17
19
26
27
29
30
31
33
35
40
41
43
44
45
46

Fragment (OE )
H

CH3

NH2

OH, NH3

CN

C2H3

C2H5, CHO

CH3NH, CH2NH2

CH3O, CH2OH

SH, CH2F;

(H2O + CH3)

Cl

CH2CN

C3H5

C3H7, CH3CO

C2H5N H

C2H5O, COOH

NO2

Mass
47

49
51
54
55
57
58
59
61
65
69
71
77
79
81
91
105
127

Fragment (OE )
CH2SH

CH2Cl

CHF2

CH2CH2CN

C4H7, C3 H3O

C4H9, C3 H5O

C3H8N

C3H7O, COOCH3;

CH2COOH

C2H5S

C2H5

CF3

C4H7O

C6H5

Br, C6H7

C6H9, C5H5O

C7H7

C7H5O, C8H9

NEUTRAL FRAGMENTS EXPELLED BY

MULTICENTERED FRAGMENTATIONS
Mass
2
17
18
20
27
28
30
31
32
34
36
42
44

Fragment (EE)
H2
NH3
H2O
HF
HCN
CO, C2H4
CH2O
CH5N
CH4O
H2S
HCI
C3H6, C2H2O
CO2

Mass
45
46
48
54
56
58
59
60
62
74
76
78
80

Fragment (EE)
C2H7N
C2H6O, or H2O+C2H4
CH4S
C4H6
C4H8, or C3H4O
C3H6O
C3H9N
C3H8O, or C2H4O2
C2H6S
C3H6O2
C6H4
C6H6
HBr

Learn about all the GC/MS Techniques

offered by Varian

Full Scan EI

Selected Ion Storage (SIS)

Chemical Ionization
(with Gas and Liquid Reagents)

MS/MS and MSn

Multiple Reaction Monitoring (MRM)

ChromatoProbe

Multi Inlet CI manifold

(Gas and Liquid)

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