Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Mass spectroscopy
Mass spectroscopy is a quantitative and qualitative analytical technique by which we can measure the molecular mass and formula of a compound and the record is known as mass spectra. Mass spectra is useful − To establish the structure of a new compound To give the exact molecular mass To give the molecular formula To indicate the presence of functional group in a compound Principle/function: The mass spectrometer is designed to perform four basic functions − • To vaporize the compound by increasing volatility. • To generate the ions from the neutral compound in resulting vapor pressure • To separate the ions according to their mass to charge ratio (m/z) in a magnetic field. • To collect the mass and record. Theory:

Molecular ion production: Mass spectrometer is a device for the production and weighing of ions. Molecules are subjected to bombardment by a stream of highenergy electrons, converting some of the molecules to ions. The molecular ions are usually radical cation and some may be radical anion.
- e+ [M] - e[M]





M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh 2.

Fragmentation: When the molecule has been bombarded by high-energy electrons to produce ions, the molecule absorbs sufficient energy and undergo fragmentation. B+ + neutral A+ C+ + neutral Decompose to produce new ions D+ + neutral


Separation of ions: The mixture of ions are separated according to the mass charge ratio in the analyzer and then recorded. The record is known as the mass spectrum. It is the record of abundance of each ion against its m/z value.


Mass spectrum: The mass spectrum is a plot of ion current intensity (ion abundance) versus m/z value. The most abundant peak will give the tallest peak of the mass spectra. This peak is known as the base peak and its mass arbitrarily assigned a value of 100%. The heaviest peak is the molecular ion peak and its mass will give the mass of the molecule.
C+ B+ Relative absorbance ↑ D A+

m/z value →


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Isotope peak: Isotopes present in the molecule may generate additional peak. Due to the occurrence of isotopes we also observe M+1, M+2, M+3 etc peaks. The relative abundances of these isotopic peaks are proportional to the abundance of the isotope in nature (e.g. the natural abundance of abundance of isotope peak is nX1.1% of the 12C containing peak. M+1 peaks are made by − 13C, 2H, 15N, 33S M+2 peaks are made by − 18O, 34S, 37Cl, 81Br)
Base peak M+ peak Relative abundance ↑ M +1 M+2

C is

1.1% of the 12C atoms. For an ion containing n number of carbon atoms, the

m/z ratio →

M+1 and M+2 peak in benzene: Benzene shows molecular ion peak at m/z value 78 due to C6H6. It will also show M+1 peak at m/z 79 due to 13CC5H6+ or, C6H5D+. M+2 peak will also show at m/z 80 due to C6H4D2+. The relative abundances of this isotopic can be used to determine molecular formula.

CC5H5D+ or, 13C2C4H6+ or,


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Atomic weight and natural abundances of some isotope − Isotope
1 2

Atomic weight 1.0078 2.014 12.000 13.003 14.003 15.0001 15.9949 16.999 17.999

Natural abundance (%) 99.985 0.015 98.9 1.1 99.64 0.36 99.8 0.04 0.2


12 13 14 15 16 17 18



Ionization method: In ionization method compound are divided into 2 groups −
a. b.

Ionization of volatile materials Ionization of nonvolatile materials


Ionization of volatile materials − Two methods are commonly used to produce ions from thermally

volatile compound --1. 2.

Electron impact ionization (IE) Chemical ionization (CI)


Electron impact ionization:

A direct probe tip is used near to a heated filament which provides electron and is heated in the ionization chamber causing vapor from the sample.


(metal sheet)

(Ceramic tip with sample)


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

• Electrons are accelerated from the hot filament to an anode, usually through a potential difference of about 70ev. • A 70ev electron has sufficient energy not only to ionize an organic molecule but also to cause extensive fragmentation. • Molecules are ionized due to bombardment with high-energy electrons by removal of an electron. The product is cation radical. M + e = M+ + 2e

Chemical ionization (CI): • In this technique a reagent gas (methane, isobutane or ammonia) is allowed to pass into the ion chamber at low pressure. • The gas is ionized by using electron impact, which can then undergo ion molecule reaction.

CH 4 + e → CH 4 • + 2e CH 4 • + CH 4 → CH 5 + + CH 3 •
+ If the sample molecules are volatilized into mixture of ions, CH 5 act


as a strong acid and protonates the sample.

M + CH 5 + → MH + + CH 4
Thus in positive ion CI-spectra, the observed m/z value is one unit greater than the true molecular weight. In CI-technique, negative ion CI-spectra may occur for molecules with electron accepting properties like trifluoroacetates, quinones and nitro compounds.


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh


Ionization of nonvolatile materials − molecules have low molecular weight but have numerous polar functional groups, or have high molecular weight; usually don’t pass into the gas phase at high temperature and at low pressure.


Field desorption:

Here, the probe tip is replaced by a thin wire on which sharp needles have been grown. The wire is supported between two posts on the probe. A solution of small amount of a sample is deposited on the wire. In the mass spectrometry the wire is maintained at +8kv and can be heated and this can cause the discharge of an electron from the sample into the metal. Thus positive ions (M+) are created. In this way molecules are thrown into the gas phase as a positive molecular ion without thermal decomposition.

• • •

Cathode slit +8KV wire (+8KV) Probe Needle Fig: Field desorption technique + + + + Ionized molecule


Desorption ionization by particles or radiation:

Laser desorption (LD) Fast atom bombardment (FAB) Californium plasma desorption Secondary ion mass spectrometry (SIMS)


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

based upon giving a large pulse of energy to the sample here intermolecular bonds are broken and the sample is desorped from its environment into the gas phase within 10-12 sec. so thermal decomposition doesn’t occur. Laser desorption → In this technique, the sample is bombarded with short duration, intense pulses of laser light. Efficient and controllable energy transfer to the sample requires resonant absorption of the molecule at the laser wavelength. Therefore, lasers emitting either in the UV or IR are employed. Laser pulses are applied for 1-100ns. One disadvantage is some thermo labile compounds may be degraded with the laser beam resulting in a spectrum of fragment ions. To overcome this problem, a matrix is used and the technique is known as matrix assisted laser desorption ionization technique (MALDI). In MALDI, a low concentration of the sample is embedded either in a liquid or a solid matrix (molar ratio 1:100 to 1:50000) which is selected to absorb strongly the laser light. In this way, the energy is transferred indirectly to the sample, and in a controlled manner which avoids sample decomposition. Used in conjunction with a suitable method for ion analysis, MALDI can give approximate molecular weight determinations for biomolecules, even in the range 100000 – 200000 Daltons. Some common MALDI matrices:
2,5-dihydroxy benzoic acid (DHB) 3,5-dimethoxy-4-hydroxy cinnamic acid (Sinapinic acid)
α-cyano-4-hydroxy cinnamic acid

Peptides, protein, lipids, oligosaccharides Peptides, protein, glycoproteins Peptides, protein, lipids, oligonucleotides



M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

FAB → Here the energy is provided by a beam of neutral atom. The sample is dissolved in a matrix of low volatility. A few µgm of the sample are dissolved in a few µl of glycerol as matrix and a beam of fast xenon atoms bombards the solution.
Bombarding atom beam

Probe Sample in matrix

sample ion

Mass analyzer

This fast xenon atoms are prepared by accelerating xenon ions and then neutralizing these ions by charge exchanger at a low pressure.

Xe+ + Xe → Xe + Xe+
Another matrixes used in FAB are ~ Thioglycerol : Diglycerol (1:1) Tetracol Teracol Glycerol Californium plasma desorption → Here the sample to be analyzed is deposited on a thin metal foil (nickel). Spontaneous fission of the radioactive Californium nucleus (252Cf) occurs, and each fission event gives rise to two fragments travelling in opposite directions. A typical pair of fission fragments are
142 18

Ba + and

106 22

Te + of high kinetic energy.

When such a high energy fission fragment passes through the sample foil, produce a high temperature of 10000K.


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Consequently the molecules in this plasma zone are desorbed from the foil with the production of both positive and negative ions. These ions are then accelerated out of the source into the analyzer system.


Cf fission Sample

+ or Ni foil (10–3 mm)

Californium plasma desorption technique produces better molecular peak for molecules having molecular weight between 10000 – 20000 Dalton.

Different technique for analyzing ions in a mass spectrometer:
a. b. c. d. e.

Magnetic sector Time of flight Quadrupole Ion cyclotron resonance Ion trap

Magnetic sector analyzer/mass analyzer: The ions may be separated according to their mass to charge ratio (m/z) using a magnetic field. Here the ions of larger mass are deflected less than the ions of smaller mass according to the equation –

m H 2r 2 = z 2v

Where, r = radius of circular of path in which ion is traveling H = magnetic field strength V= potential difference of ion.


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

The equation clarifies that by varying the magnetic field strength or accelerating potential, the ions of all m/z value can be successively allowed to pass through the detector slit & mass spectrum recorded. Time of flight mass analyzer: TOF mass analyzer separates or resolves the ion beam by measuring the flight time of the ions. The technique requires that all the ions produced in the ion source should leave at the same time. The ions are accelerated by a potential difference and then allowed to pass into the filed free region. Since all the singly charged ions will acquire the same kinetic energy, the largest mass will have the lowest velocity and the longest time of flight over a given distance. Mathematically,
m 1 t=L × e 2V
where t = time of flight L = distance in which a ion travel m = mass of the ion e = charge of the ion V = velocity in which the ion travel

It is quicker than any other mass analyzer and applicable for all masses. Quadrupole: Here four parallel rods arranged symmetrically around an ion flight path and a direct current and a radio frequency are applied to the rods resulting an oscillating electrostatic field. The ions when pass through the region, will acquire an oscillation in the electrostatic field. The ions of incorrect m/z ratio undergo an unstable oscillation and strikes one of the rods. Ions of correct m/z ratio undergo stable oscillation of constant amplitude and pass through analyzer to reach the recorder. Quadrupole inexpensive. analyzer is a relatively compact instrument and


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Low-resolution mass spectrometer (LRMS): LRMS employs a single stage analyzer. It resolves only integral masses and it can’t differentiate the molecules e.g. CO (28), CH2=CH2 (28), N2 (28). As all have the same integral mass 28. since it can’t give exact masses molecular formula can’t be determined. High-resolution mass spectrometer (HRMS): HRMS employs multiple stage analyzer such as magnetic and quadropole sectors linked in series. The accuracy of these types of instruments enables the distinction between different isotopes such as

C vs.


C. The high-resolution data are obtained at an accuracy of

0.0001 amu (atomic mass unit) and consequently this permits a distinction between species of the same mass unit such as - CO (28), CH2=CH2 (28), N2 (28). Therefore data from HRMS are essential for unambiguous determination of molecular data.

Double focusing mass spectrometer are used to obtain high resolution in which the beam ions are pass through an electric field region before entering the magnetic field. In a single focusing mass spectrometer, there is a lack of uniformity of ion energies that is all ions do not have precisely same velocity. The result is peak broadening and low to moderate resolution.

Electrospray ionization (ESI): ‘Electrospray’ is applied to the small flow of liquid (1-10µl/min) from a capillary needle when a potential difference of 3-6kV is typically applied between the end of the capillary and a cylindrical electrode located 0.3-2 cm away. Under these circumstances, the liquid leaving the capillary does not leave as a drop, but rather as a spray.


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

The spray consists of highly charged liquid droplets, and these droplets may be positively or negatively charged depending on the sign of the voltage applied to the capillary. If the liquid spraying from the capillary contains sample molecules, then a molecular ion of these sample molecules can be obtained by evaporation of the solvent. ESI is an excellent technique for the production of molecular ions from large polar molecules, and it will be seen subsequently that, since it frequently produces multiply charged ions, it is a very powerful tool in the analysis of biopolymers. This is especially true since the method can be conveniently used to analyze directly the effluent from an HPLC column. Gas chromatography-mass spectrometry (GC/MS) The separation and detection of components from a mixture of organic compound is readily achievable by gas chromatography. Furthermore, limited characterization of unknown components is often possible from retention times appropriate to the particular column used. Mass spectrometry, because of its high sensitivity and fast scan speeds, is the technique most suited to provide definite structural information from the small quantities of material eluted from a gas chromatograph. The association of the two techniques provided a powerful means of structure identification for the components of natural and synthetic organic mixtures even though the components may be present in nanogram quantities and eluted over periods of only a few seconds. The interface between the GC and the MS is a jet separator. Such a combination is useful as an aid in determining the structures and chiralities of amino acids. The amino acids are first derivatized as


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

follows: by treatment with trifluoroacetic anhydride in the first step and by isopropanol / HCl in the second (to render them volatile): NH2CH(R)COOH → CF3CONHCH(R)COOH → CF3CONHCH(R)COOCH(CH3)2 Since trifluoroacetyl is a good electron capture group, the mass spectra are determined in the negative ion mode. The mixture of derivatized amino acids (frequently from 6N HCl hydrolysis) is simply injected on to a chiral GC column, where the retention times are not only dependent on structure but also on absolute configuration of the amino acids. Thus separation, molecular weight, and chirality can all be determined in one experiment. Liquid chromatography-mass spectrometer (LC/MS) • HPLC is a powerful method for the separation of complex mixtures, especially when many of the components may have similar polarities. In reverse-phase HPLC, the column substrate is such that starting with an aqueous solution of a mixture of polar components; the most polar components are eluated first. The later-eluated hydrophobic components are often encouraged to leave the column by gradually increasing the concentration of acetonitrile (CH3CN) in the otherwise aqueous developing solvent. • If the mass spectrum of each component can be recorded as it eluates from the HPLC column, quick characterization of the components is greatly facilitated. Tandem mass spectrometry (MS/MS): • Tandem mass spectrometer uses two mass spectrometers is tandem. • It has a great potential value in the structure elucidation of organic compounds.


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

• In this technique, a compound to be analyzed is subjected to ionization and fragmentation. The mixtures of ions are then separated in the first mass analyzer. • From the mixture of ions, a specified ion is selected for the second mass analyzer. The magnetic field is set to pass only the selected ion through a slit into a collision chamber. This chamber contains a high energy reagent gas like helium (He) or argon (Ar) with which the ions collide. As a result, mixtures of ions are produced. The process is known as collision activated decomposition (CAD). The ions are then analyzed in the second mass analyzer. Example – Penazitidine A is a heterocyclic compound with a long chain. It has a methyl group on the side chain but the position was not established by various technique (NMR & even by 2D NMR). But MS-MS can determine the position of methyl group on the structure. The ion at m/z 296 was selected. It was allowed to pass into the collision chamber where it is subjected to CAD. The mixtures of ions produced are analyzed in the 2nd mass analyzer. The intense peak at m/z 182, m/z 210 indicates the position of methyl group at C12 of the side chain. Fragmentation patterns: For most classes of compounds, the mode of fragmentation is somewhat characteristic. The most common mode of fragmentation involves the cleavage of one bond. In this process the odd-electron molecular ion yields an odd-electron neutral fragment (a radical) and an even electron fragment ion (carbonium type)


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Fragmentation via the cleavage of one bond:

[R − CH ]

+ •

→ R + + • CH 3
+ •

→ + X • [odd elecetron radical] R+ [old electron molecular ion] [evene electron fragment ion]

[R − X ]

where, X = halogen, OR, SR or NR2, R = H, alkyl or aryl

Fragmentation via the cleavage of two bonds:

[RCH − CHR ]

+ •

→ [RCH = CHR / ]•


+ H 2O
+ •


• 2 − O − C − CH3 ] →

[RCH = CH ]


HO − C − CH3 (evenelectronneutralfragment)

(odd electronmolecularion)

(odd electronfragmentio n)

In addition to this process, fragmentation process involving rearrangements, migrations of groups and secondary fragmentations of fragment ions are also possible. Fragmentation patterns of different classes of compound:
Name of M+ peak compound M+ peak is observed but less Alkane − i) Branched intense than straight chain chain hydro- compound carbon. + e.g. [CH 3 − CH − CH 3 ]∗ Isobutane CH3 CH3-CH-CH3 Fragmentation C-C bonds leading to the formation of 20 & 30 carbonium ions which are more stable than 10. As a result the M+ ion will become less intense and undergo further fragmentation. • Cleavage of a C-C bond yields an isopropyl carbonium ion.



− CH


+ •

CH3 2 carbonium ion, m/z =43


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Alkanes − ii)Straight chain compound e.g. − Butane

Molecular ion peak observed at C-C bonds breaks resulting in a homologous m/z = 58 series of fragmentation products. Primary carbonium ion is formed. + 1. Cleavage of C-1 to C-2 bond result in loss of [CH 3 − CH 2 − CH 2 − CH 3 ]• a Me-radical and formation of propyl carbonium ion. 43

[CH 3 − CH 2 − CH 2 ]+ + [CH 3 ]•

(m/z = 43)

29 15 58

Cleavage of c-2 to c-3 bond result in loss of a Et-radical and formation of ethyl carbonium ion

[CH 3 − CH 2 ]+ + [CH 3 − CH 2 ]•

(m/z = 29)


15 25 30 40 45 50 55 60

Cleavage of c-3 to c-4 bond results in loss of a propyl radical and formation of methyl carbonium ion

(m/z) → Fig: Mass spectrum of Butane Alkenes − E.g. − 1-butene & 2-butene CH2=CH-CH2CH3 1-butene Distinction M+ peak • 1-butene and 2-butene give molecular peak at m/z =56. • Both produce allyl carbonium ion at m/z = 41.

[CH 3 ]+ + [CH 3 − CH 2 − CH 2 ]•

(m/z = 15)

Alkene isomers show nearly identical mass spectra. So double bond can’t be located. Also cis & trans can’t be differentiated.

[R − CH

• + • 2 − CH = CH 2 ] → R + CH2 − CH = CH 2


[CH 2 = CH − CH 2 − CH 2 − R ]• → R • + [CH 2 CH 2 − CH = CH 2 ↔ CH 2 = CHCH 2 − CH 2


Alkynes − E.g.− Propyne


= CH− CH2 − CH3 ]• → CH3 + CH2 = CH− CH2



(m/z = 41) • Molecular ion peak is [H − C ≡ C − CH 2 − R] → R • + rather intense. + • Give molecular ion peak at m/z = 40
[H − C ≡ C − C H 2 ↔ HC = C = C H 2 ]
+ +   →  HC = C C H 2 ↔ H C = C = CH 2    (m/z = 39)
+ •

[HC ≡ C − CH 3 ]•



M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Aromatic hydrocarbon i) containing alkyl group E.g. Tolune

• Show distinct and intense Fragmentation occurs at benzylic position not at phenolic position. molecular ion peak.

• Not so intense

Fragmentation occurs at benzylic position. Loss of • Shows very intense hydrogen gives a strong peak at m/z = 91 molecular ion peak at m/z = 92
+ CH3

+ CH2 + C7H7 Benzyl carbonium ion (m/z = 91)


Tropylium ion (m/z = 91)

Ethyl benzene

Molecular ion peak gives at Fragmentation occurs at benzylic position. Loss of m/z = 106 hydrogen gives a strong peak at m/z = 91
+ CH2
+ CH2-CH3

+ CH3


Propyl benzene

Molecular ion peak at m/z = Fragmentation occurs at benzylic position. Loss of 120 hydrogen gives a strong peak at m/z = 91
+ CH2-CH2-CH3

+ CH2 + CH2-CH3


Alcohol 1º & 2º 3º

Intensity of molecular ion • peak is usually low.

Loss of an alkyl group. C-C bond broken.
CH3 − CH2 − C H 2 + CH2 = OH+ m/z=31

[CH3 − CH2 − CH2 − CH2 − OH] • (1 − butanol)

CH3 − C H 2 + CH3 - CH = OH+ m/z=45

[CH3 − CH2 − CH − OH]• CH3 (2 − butanol)

C H 3 + (CH3 ) 2 - C = OH+ m/z=45


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh


Dehydration: the importance of dehydration increases as the chain length increases. The dehydration is a 1,2 elimination of water.


General reaction (CH2)n RCH H CHR' OH RCH (CH2)n + H2O CHR'

Example - (1-butanol) (CH2)2 CH2 H CH2 OH CH2 CH2 + H2O CH2

Simultaneous loss of water & alkene usually which contains more than four carbon.
+ H RCH H2C C H2 H O CH2 + R C H CH2 + CH2=CH2 + H2O

Ex − 1-butanol −
H O H2C H2C C H2 H CH2 H2C CH2 + + + CH2=CH2 + H2O

m/z = 28

Phenols − E.g.−Benzyl alcohol

Exhibit intense molecular ion • Loss of CO peak. 108 H H OH CO (M) 79 107 77
+ CH2OH OH + + H m/z=107

m/z = 66

H - CO

H + C6H5 + H2 m/z = 77


Fig: Mass spectrum of benzyl alcohol


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Ethers −

Weak molecular ion peak.

Loss of alkyl group/cleavage of C−C bond to the α-carbon
[R − C H 2 OR' ] → CH 2 = O R'+ R •
α + • +

Cleavage of C−O bond
[R − C H 2 OR' ]• → C H 2 − R + R' O •
α + +

Aromatic ethers − E.g. − Anisole

Molecular observed



is •

Loss of alkyl group

[C 6 H 5 OR]• → C 6 H 5 O + R •


Loss of alkoxy group

[C 6 H 5 OR]• → C 6 H 5


+ OR •

Example − Anisole

[C 6 H 5 - O - CH 3 ]• → C 6 H 5 O + CH 3


[C 6 H 5 - O - CH 3 ]• → C 6 H 5


+ OCH 3

Aliphatic aldehyde −




is •

α-Cleavage: cleavage occurs in one of the two bonds to the carbonyl group.
O R C H H C O +

observed/ weak






+ H *


R *


* +R+

• •

β-Cleavage: cleavage occurs in β- carbon.
R − CH 2 − CHO → R + + CH 2 = CHO •

Mclafferty rearrangement: when alkyl group attached to the carbonyl carbon is large, a type of rearrangement called Mclafferty rearrangement occurs.
+ H R1 R2 CH CH C CH2 H O R 1 -C H + R 2C H C H2 C H -O H m /z=4 4 +


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

e.g. mass spectrum of Butyraldehyde: molecular ion peak at m/z=72.
O CH3-CH2-CH2-C-H + + + CH3CH2CH2=O + H H-C + O + CH3CH2CH2 m/z=71 m/z=29

O CH3-CH2-CH2-C-H +

+ CH3CH2 + CH2=CHO


β - Cleavage:
Mclafferty rearrangement:
CH2 CH2 CH2 H O CH + + CH2 + CH2 + CH2 CH -OH m/z=44

Aromatic aldehyde − e.g. Benzaldehyde

• •

Intense molecular ion peak. Benzaldehyde show molecular peak at m/z = 106

Loss of hydrogen show molecular peak at m/z = 105
O C H + C + O +H m/z=105

106(M+) 105 77 C6H5+ C6H5C≡O+ •

Loss of CHO group may lead to C6H5+ which show molecular peak at m/z = 77

Aromatic ketones −

Fig: mass spectrum of Benzaldehyde Intensed molecular ion peak

loss of alkyl radical giving ArCO+ ( α Cleavage)
O C R m/z=105 + C + O +R* + m/z=77

loss of COR rearrangement)
H O C CH2 R CH CH2 +




C CH2 m/z=105

+ O

m/z=120 + CHR CH2


M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Acyclic Ketones −

• Intense peak.




+ O R - -- C -- - R '
+ O R --- C ---R ' R '- C + O + R *

R -C

+ * O + R'


Mclafferty rearrangement:
+ R 1C H R 2C H CH2 H O CR3
+ O CH3-C-CH2CH3 + CH3-C O m/z=43 + CH3CH2

R 1 CH + R 2C H



e.g.− 2-butanone

larger gr. will be predominant

+ O CH3--C-CH2CH3 CH3CH2-C m/z=57 + O + CH3

the peak at m/z =43 is more intense than the peak at m/z =57 Aliphatic amines − May be very weak or even absent.

β - Cleavage:
+ R-CH2-NH2 * + R * + CH2 NH2 m/z=30

Aromatic amines −

Intense molecular ion peak

Loss of hydrogen atom.
NH2 + * + NH * H* m/z=92 * HCN m/z=66 H H + * H + * + H* m/z=65

Aromatic Carboxylic acids −

Intensed molecular ion peak

Loss of OH to form C6H5CO+ ion (m/z = 105) followed by loss of CO to form the C6H5+ ion
O C OH + * + C O + * +

m/z=105 + OH *



M. Kaisarul Islam, Lecturer, Department of Pharmacy, Jagannath University, Dhaka-1100, Bangladesh

Weak molecular ion peak Aromatic 105 esters − E.g. − Methyl benzoate. 77 136 + (M )

α - Cleavage gives to the formation of C6H5CO+
O C OCH3 + * + C m/z=105 + OCH3* O + m/z=77

Fig: mass spectrum of methyl benzoate Esters − Weak but noticeable ion peak • α-Cleavage: loss of the alkoxy group to form corresponding
O R C-OR '
+ O


+ O








O + R







+ O




β-Cleavage: Mclafferty rearrangement
H R1CH R2CH CH2 O C OR' + * OH R1CH + R2CH C OR' CH2 + *


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