Mass Spectroscopy- Definition, Principle, Reactions, Terms, Uses

Mass spectroscopy is the accurate method for determining of molecular mass of the compound and its elemental composition.

Mass Spectroscopy
Mass Spectroscopy

Principle of Mass Spectroscopy

When molecules are bombarded with an energetic electron beam, 1e- is removed from the molecule. The removal of electron e- from a molecule causes the molecule to become positively charged, resulting in the formation of a molecular ion. Further fragmentation of molecular ions produces daughter ions.

Each ion has its particular mass-to-charge ratio (i.e. m/z). They are separated according to their m/z ratio and give a mass spectrum. m/z vs abundance gives the mass spectrum.

Different terms involved in the mass spectrum

A mass spectrum is a record of the masses and relative abundances of the ions. The m/z ratios are taken along the abscissa, while the relative abundances (intensity) are taken along the ordinate.

Fig1: Mass spectrum of carbon dioxide
  • Base peak: It is the highest peak or more intense peak in the spectrum.
  • Molecular ion peak: Molecular ion is also called the parent ion and is usually designated as M+. , a positively charged molecule with an unpaired electron. The mass of the parent ion gives the molecular mass of the sample.

In a few cases, the parent ion peak may be the base peak and can be easily recognized. In most cases, the parent ion peak is not a base peak and has a very small abundance.

Some features of molecular ion peak:

  1. The molecular ion peak in aromatic compounds is relatively much intense due to the presence of a π-electron system.
  2. Conjugated olefines show a more intense molecular ion peak as compared to the corresponding non-conjugated olefins with the same number of unsaturation.
  3. Unsaturated compounds give a more intense peak as compared to saturated or cyclic molecules.
  4. The relative abundance of molecular ion peaks of straight chain compounds is more than the corresponding branched-chain compound with the same number of carbon atoms. for example, the molecular ion peak for n-pentane is more intense than that of neopentane.
  5. The absence of a molecular ion peak in the mass spectrum means that the compound under examination is a highly branched or tertiary alcohol.
  • Fragment ion peak: The ions formed by the fragmentation of molecular ions or other ions in a mass spectrometer give a different peak in the mass spectrum. These are called fragment ion peaks. The peak of fragment ions provides information that can be used to identify unknown compounds.
  • Metastable ion: Metastable ions are the ions that fragment slowly after the emergence from the ion source but before they reach the detector. They are thus displaced from the position in the mass spectrum, which would correspond to their true masses. Peak arises due to the metastable ions being normally broad and of low intensity. Such metastable peaks appear at noninteger masses.

If the ions (molecular or fragment) M+ are accelerated before their breakdown then they may decompose in the accelerating chamber into M2+ and M3, and part of the kinetic energy of M1+ is lost to the neutral fragment M3. M2+ is continuous to accelerated and collected.

M2+ produced in this way is not recorded as mass M2 but recorded as M*,

where M*= M22/M1

M* is called metastable ions and is usually recorded as a weak broad peak of low intensity.

These metastable peaks are observed primarily when the lifetime of original species M is in the range of 10-4 – 10-6 sec, long enough to reach the accelerating region but not long enough to become fully accelerated. The recognition of metastable ions helps in the prediction of the position of parent ions and daughter ions and in determining both the original mass and size of the ejected fragment. hence it is useful for deducing the fragmentation mechanism.

Characteristics of these peaks are as follows:

  1. They don’t necessarily occur at the integral m/z value.
  2. These are much broader than the normal peaks.
  3. These are of relatively low abundance.

Nitrogen Rule

Nitrogen-containing compounds with an odd number of nitrogen atoms in the molecule must have an odd molecular mass. An even number of nitrogen atoms or the absence of nitrogen in the molecule show the molecular mass of the compound must be even. For the nitrogen rule to hold only unit atomic masses (i.e., integers are used in calculating the formula masses). This rule holds for all compounds containing carbon, hydrogen, oxygen, nitrogen, sulfur, and halogen, as well as many of the less usual atoms such as phosphorous, boron, and arsenic.

General fragmentation modes:

The relative abundance of the fragment ions formed depends upon the following factors:

  1. Stability of ions
  2. Stability of radical lost

the stability of the ions can be judged by stabilization of the charge, which depends upon;

a. Resonance

b. Inductive effect

c. Polarisability and so on

Some important fragmentation mods are:

Simple cleavage

Fragmentation of odd electron molecular ion M+. may occur through homolytic or heterolytic cleavage of single bond.

A. Homolytic cleavage:

Odd electron ions have an unpaired electron which is capable of new bond formation. The energy released by bond formation can help offset the energy required for the cleavage of some other bond in the molecules.

Homolytic cleavage reactions are very common and can be classified in the following steps:

Mode I: This type of fragmentation mode operates in compounds in which the heteroatom is singly bonded to a carbon atom. In this mode, the parent ions are formed by the removal of one electron from the heteroatom. A new bond is formed with an adjacent atom through the donation of an unpaired electron and the transfer of an electron from the adjacent bond.

More abundant peaks are formed by the cleavage of the C-C bond, which is in the α position to the heteroatom in mass spectra of alcohol, amines, and ethers.

Mode II: when a heteroatom is bonded to the carbon atom by the double bond, α-cleavage is the preferred fragmentation mode.

This type of fragmentation is shown by many compounds such as ketone, and ester amide. In ketones, significant peaks are obtained due to cleavage of the C-C bond, which is alpha to the carbonyl bond. Unsymmetrical ketones show two types of peaks since either alkyl group can lose. The higher alkyl radical is usually preferred.

B. Heterolytic cleavage

Cleavage of the C-X (x= O, N, S, Cl) bond is more difficult than that of the C-C bond. In such a cleavage the positive charge is carried by the carbon atom and not by a heteroatom. eg. Fragmentation of alkyl halide.

In the spectra of monohalogenated compounds, hydrocarbon ions are formed in more abundance. As the size of the halogen atom increases, the C-X bond becomes weak, so alkyl bromide and iodides are easily broken, while alkyl chloride is less susceptible to fragmentation.

Retro-Diel’s Alder reaction

It is the characteristic of cyclic olefins, which involve multicentered fragmentation. It involves the cleavage of two bonds of the cyclic system resulting in the formation of two stable unsaturated fragments in which two new binds are formed. This process is not accompanied by any hydrogen transfer rearrangements.

The highly substituted or more conjugated fragment, which has low ionization energy, carries a charge.

Rearrangement reactions

Rearrangement ions are fragments whose origin can’t be described by simple cleavage of bond in the molecular ion but are a result of intramolecular atomic rearrangement during fragmentation.

  • Rearrangement resulting in the elimination of stable neutral molecules is common.
  • The rearrangement peak can be recognized by considering the m/z number of fragments ions and their corresponding molecular ion.
  • An even-numbered peak derived from even-numbered molecular ions is the result of two cleavages, which may involve a rearrangement.

Different modes of rearrangements

A. Hydrogen transfer

These processes are very common in mass spectroscopy, which involves the transfer of hydrogen atoms from one part of the molecule to another part. E.g., an even-numbered fragment mass from an even-numbered molecular ion mass indicates a rearrangement of hydrogen has accompanied the fragmentation process.

From hydrogen rearrangement, we can distinguish between cis and trans isomer as well as ortho-substituted compounds from meta and para-substituted compounds.

B. γ -hydrogen transfer (Mc-Lafferty rearrangement)

This arrangement involves the cleavage of the β-bond followed by the γ-Hydrogen transfer. The mechanism involves the six-membered transition state. This rearrangement eliminates neutral molecules from aldehydes, ketones, amines, and unsaturated compounds.

To undergo the Mc-Lafferty rearrangement reaction, a molecule must possess appropriately located heteroatoms (e.g., oxygen), a π system, and an abstractable hydrogen atom at γ position to the C=O system.

such arrangement often accounts for prominent characteristic peaks and is consequently very useful. They can frequently be rationalized on the basis of low energy transitions and increased stability of the product.

MC-Lafferty rearrangement reaction

C. Random rearrangement: Random rearrangement of hydrocarbon was noted by early mass spectrometers in the petroleum industry.

Application of mass spectroscopy

  • It is used to determine the molecular weight of compounds.
  • In organic chemistry, mass spectroscopy is used to determine the structure of complicated compounds.
  • Mass spectroscopy is used for the qualitative and quantitative study of compounds.
  • It is also used for the detection of impurities.
  • Mass spectroscopy is used in the study of drug metabolism study, and also has clinical, toxicological, and forensic applications.
  • It is used in the isotope ratio determination and carbon dating process.


  1. Silverstein, R. M., Webster, F. X., & Kiemle, D. J. (2005). Spectrometric identification of organic compounds. Hoboken, NJ: John Wiley & Sons.

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