A mass spectrum (MS) is a graphical representation of the relative abundance of ions at different mass-to-charge ratios (m/z) in a sample. Mass spectrometry is a powerful analytical technique used to identify and characterize the chemical composition of a wide range of substances, including organic compounds, proteins, peptides, and even small molecules. Here's how a typical mass spectrum is generated and what it can tell you: Ionization: In mass spectrometry, the sample is first ionized, meaning that the atoms or molecules are converted into ions (charged particles). Common ionization methods include electron impact, electrospray ionization, and matrix-assisted laser desorption/ionization (MALDI). Mass-to-Charge Ratio (m/z): After ionization, the ions are separated based on their mass-to-charge ratio (m/z). This ratio is a dimensionless quantity, and it represents the mass of the ion (in atomic mass units, amu) divided by its charge (in elementary charge units, e). Ion Separation: The ions are separated by a mass analyzer, such as a magnetic sector, time-of-flight (TOF), quadrupole, or ion trap, depending on the specific instrument used. The mass analyzer sorts ions according to their m/z values. Detector: As the ions exit the mass analyzer, they are detected, and their abundance is recorded. The detector measures the number of ions at each m/z value. Data Output: The data from the detector is then used to create a mass spectrum. The x-axis of the mass spectrum represents m/z values, while the y-axis represents the relative abundance or intensity of ions at each m/z value. A typical mass spectrum might have peaks at specific m/z values, and these peaks can provide valuable information about the sample: Base Peak: The peak with the highest intensity in the spectrum is called the base peak. It represents the most abundant ion. Molecular Ion Peak: The peak at the highest m/z value (farthest to the right) often represents the molecular ion, which can provide insight into the molecular weight of the compound. Fragment Peaks: Peaks at lower m/z values are often fragment ions resulting from the breaking of chemical bonds within the original ions. These fragment ions can provide information about the structure of the compound. Isotopic Peaks: Some elements have natural isotopes, and their presence can result in multiple peaks with slightly different m/z values. These isotopic peaks can also provide information about the composition of the sample. Interpreting a mass spectrum involves analyzing the positions and intensities of these peaks to identify the compound and its structure. Mass spectrometry is widely used in various fields, including chemistry, biochemistry, environmental science, and forensic analysis, for tasks such as identifying unknown substances, quantifying the amounts of specific compounds, and studying chemical reactions.

1. Mass spectrometry
Mass spectrometry is a powerful analytical
technique used to quantify known materials, to
identify unknown compounds within a sample,
and to elucidate the structure and chemical
properties of different molecules.
The complete process involves the conversion
of the sample into gaseous ions, with or
without fragmentation, which are then
characterized by their mass to charge ratios
(m/z) and relative abundances.

2. Components of a Mass Spectrometer
The instrument consists of three major components:
Ion Source: For producing gaseous ions from the substance being studied.
Analyzer : For resolving the ions into their characteristics mass
components according to their mass to charge ratio.
Detector : For detecting the ions and recording the relative abundance of
each of the resolved ionic species

3. With all the above components, a mass spectrometer should
always perform the following processes:
Produce ions from the sample in the ionization source.
Separate these ions according to their mass-to-charge ratio in the
mass analyzer.
Eventually, fragment the selected ions and analyze the fragments
in a second analyzer.
Detect the ions emerging from the last analyzer and measure their
abundance with the detector that converts the ions into electrical
signals.
Process the signals from the detector that are transmitted to the
computer and control the instrument using feedback.

4. Analysis of compounds by MS spectrum
Parent Peak
(M+)
Base Peak
Metastable Peak
(M*)
(m/e)

5. CH3 m/e = 114
a
CH3
H2
H2
H2
H3C
C
C
C
C
CH3
b
CH3
CH3
H
H
H 2
2
2
C
C
C
C
CH 3
m/e = 99
a
3
H
C C
CH3
CH3
H2
H2
H2C
C
C
CH3
m/e = 57
b
+ CH3
+
Fragmentation of molecule via MS

6. R
H 2
C C
H
C H 2 2 H
C C
H
C H 2 +
R
allyl g r o u p m / e = 4 1

7. H2
R
C
C
CH 2 H C
C
CH +
R
propargyl group m/e = 39

8. R
C
C
X
H
Odd-electron ion (Radical Cation)
R
C
C
H
Carbocation
-bond
Cleavage at
-bond
R
C
H
C
X C
X
R
C
C
Odd-electron
ion
(Radical Cation)
- X
- HX

9. Methyl Chloride (CH3Cl, M. Wt. = 50)

10. Methyl Bromide (CH3Br, M. Wt. = 94)

11. (Aromatic hyrdrocarbons)
H2C
R
R = H, CH3, C2H5, .....
CH2
-R
benzyl cation
m/e = 91
tropylium ion
m/e = 65
+
HC
CH

12. Alcohols R-OH:
R
H2
C
OH H2C
OH H2C
OH
m/z 31
Primary alcohols
- R
H2C
OH O O
- H - CO
H
m/z 107 m/z 79 m/z 77
H
H
H
H
m/z 108
Benzyl alcohol
- H2

13. Phenols:
O H
- C O
H
H
m / e = 6 6
H
m / e = 6 5
- H
m / e = 9 4
P h e n o l

14. Aldehydes and Ketones :
Cleavage at both side of carbonyl group
- R
- H
O
C
H
m/z 29
R
C
O M
- 1
- R
- R`
O
C
R`
R
C
O
O
R
C
H
Aldehydes
O
R
C
R`
Ketones
H
O
C
- H - CO
- Ph
m/z 106
m/z 105 m/z 77
O
C
H
m/z 29
- C2H2
C H4
3
m/z 51
C
O

15. O
H 3 C H 2 C
C
C H 2 C H 3
- C H 2 C H 3
3 - p e n t a n o n e
O
C
C H 2 C H 3
m / e = 5 7
O
C
C H 2 C H 3
C H 2 C H 3
m / e = 2 9

16. McLafferty type cleavage (ϒ-Hydrogen Rearrangement)
When the alkyl group attached to carbonyl group contain at least 3-carbon
atoms (ϒ- carbon atom) it will carry out McLafferty type cleavage through ϒ -H
migration
followed
pentanone
H 2 C
H 2
O
by
elimination
H
R 1
R 2
C H 2
of
alkene
R 1
C H
H 2 C
at
β-bond
as
shown
in
2-
H
O
R 2
C 

 C H
H 2 C
H 2
O
H
C H 3
C H 2
C H 2
H 2 C
O
H
C H 3
C 


H 2 C

17. CYCLOHEXANONE-TYPE REARRANGEMENT:
Cyclohexanone is a ketone, the most likely fragmentation to occur after
initial ionization at the O atom is -cleavage on either side of the carbonyl
group. This cleavage involves no loss of mass. The spectrum of
cyclohexanone shows the peak at m/z 83, representing the loss of CH3, as
well as those at m/z 69 (loss of CH2CH3), m/z 55 (base peak), m/z 70 (losses
of CH2=CH2 or CO), and m/z 43 (losses of CH2=CH2 and CO).
m / e = 9 8
O
CH 2
O
H
C H 3
O
O
m / e = 5 5
CH 3
H 2 C
O
m / e = 8 3
+ H 2 C
CH 3 C H 3
+
m / e = 6 9
O

18. Acids and Esters:
O
R
C
OH
- R
- OH
O
C
OH
m/z 45
R
C
O M
- 17
- R
- OR`
O
C
OR`
R
C
O
Acids
O
R
C
OR`
Esters

19. - CH3
- OCH3
O
C
OCH3
C
O
3
H C
m/e = 59
m/e = 43
O
H3 C
C
OCH3
Methyl acetate
m/e = 74

20. O
C
O C H 3
- O C H 3
m / e = 1 0 5
Methyl be nz oa t e
m / e = 1 3 6
C O
McLafferty type cleavage:
H2C
H
CH
CH2
H2C
O
H
OH
C 
OH


CH
O
H2
Hexanoic Acid
H3CH2C
H3CH2C

21. H2 C
H2
O
H
CH2
CH2
H2 C
O
H
OCH2 CH3
C 
OCH2 CH3


H2 C
Ethyl butanoate
2
CH2
O
H
H3 CH2 CH2 C
O 

C H
C H 2
CH2
O
O
H
H3 CH2 CH2 C
Ethyl butanoate
H 2 C
H 2
O
H
H 2 C
O
H
C 
O C 4 H 9


C H
B u t y l p a l m i t a t e
C H 2
O
O
H
C
H 1 5
3 1


C H
O
O
H
C 1 5 H 3 1
C 1 2 H 2 5
C H 2


C H
C 1 2 H 2 5
O C 4 H 9
m / e = 1 1 6
C 2 H 5
C H 2


H C
C 2 H 5
B u t y l p a l m i t a t e
m / e = 2 5 6

22. Cyclohexene Derivatives (Retro Diels-Alder Fragmentation:
2
H C
2
H C
C harge
Retention
2
H C
H 2 C
+
H 2 C
CH 2
H 2 C
H2 C
+
2
H C
CH2
C harge
migration

23. Limonene [1-methyl-4-(2-propenyl)cyclohexene]
Charge
Retention
migration
H3C
Limonene
m/e = 136
H3C H3C
Charge
CH2
H3C
m/e = 68
CH2
H3C
H2C
m/e = 68

24. The mass spectra of 3-phenyl-1-cyclohexene and 4-pheny-1-cyclohexene show
quite different responses to the retro Diels-Alder reaction. The 4-phenyl
isomer produces either butadiene (m/z 54) or styrene (m/z 104) fragments,
with the latter preferred because of its lower IE. Fragmentation pathway
prefers charge migration with lower ionization energy, so fragment 104 is more
predominate.
Charge
Retention
migration
Ph
4-Phenyl-1-cyclohexene
m/e = 158
Ph CH2
Ph
Charge
Ph
m/e = 54
Ph CH2
m/e = 104
H2C
+
IE = 9.1
+
IE = 8.4

25. On the other hand, 3-Phenyl-1- cyclohexene, produces either ethylene (m/z
28) or 1-phenylbutadiene (m/z 130) fragments. Fragmentation pathway
prefers charge retention with lower ionization energy, so fragment 130 is
more predominate.
Charge
Retention
Charge
Ph
3-Phenyl-1-cyclohexene
m/e = 158
Ph Ph
H2C
H
2
IE lower
than 8
H2C
C
+
C
H
2
m/e =
130
Ph
IE = 10.5
migration
H2C
CH2
m/e = 28
+
CH2
Ph