Mass Spectrometry

Mass spectrometry is an impressive analytical technique used for identification and quantification of wide range of chemical and biochemical compounds. This technique is subtle enough to detect minor mass changes in the compounds, allowing for their structural elucidation. In mass spectrometry, molecules are converted into gaseous phase ions and separated on the basis of their mass-to-charge ratio (m/z). The ions move towards the detector under the effect of magnetic and electric field and get segregated as per their m/z ratio. The result is achieved in form of a mass spectrum which represents the relative abundance versus m/z ratio of a sample.

Central Analytical Mass Spectrometry Facility

Also Read: QnA on Mass Spectrometry


The analyte molecules are converted to gaseous phase and bombarded with high speed electrons so that they are ionized.

M + e- =M+ + 2e

These ions are separated in space or time, based on their mass-to-charge ratio and are quantified. All the ions are accelerated across the same distance by same force, therefore have same kinetic energy (KE), determined by the acceleration voltage of the instrument (V) and the charge of the ion (z), given as:

KE = z V = ½ m v2

m = mass of ion
v = velocity of ion

Mass spectrometry generates multiple ions from the sample under investigation then it separated them according to their specific mass to charge ratio and then records the relative abundance of each ion type.


• Ionization
• Acceleration
• Deflection
• Detection


Ionization is done by making the sample volatile directly in the source within the vacuum. The gas molecule phase is bombarded with electrons generated from a heated filament at opposite voltage to that of the source. This technique is commonly known as hard ionization because it causes the ion to fragment. It is most common for GCMS.

Fast Atom Bombardment
It is the technique which is popular in the nineties. It was done by bombarding the sample mixed in metrics commonly glycerol and nitrobenzoic acid by argon and xenon. The metrics allow the sample to refresh itself. This technique is considered a soft ionization technique.

Electron Spray Ionization (ESI)
It is the most popular technique where electrospray is created by putting high voltage on a flow of liquid at atmospheric pressure. This spray is directed to an opening of the vacuum system of the mass spectrometry where the droplets are desolvated by the combination of heat, vacuum, and accelerated into gases. Eventually, the ions are rejected from the droplets and are accelerated into the mass analyzer.

Atmospheric Pressure Chemical Ionization (APCI)
This technique is similar to electron spray ionization but instead of putting voltage to the spray itself. The voltage is placed on the needle creating a discharge mostly of hydronium ions. The sample is injected into this discharge using a spray of liquid with hot gases that volatilize the sample. The ions with hot gases volatilize the sample. The ions are formed by protons transferred by hydrogen ions.

Matrix-assisted Laser Desorption Ionization (MALDI)
It is the technique of ionization in which the sample is bombarded with a laser. The sample is mixed with a matrix that will absorb laser and transfer a proton to the sample MALDI is mostly performed for TOF instruments.


The ions are propelled away from a very positive charge ionization chamber. These ions are then passed through three slits having different voltages. The ion being is now accelerated and focused a fine stream of ions.


Different ions are deflected by the different amounts and the amount of deflection depends upon;

Mass of the ion Lighter was deflected more and heavier will deflect less.

Charge of the ion More charge, deflection increase.

There is a two-factor combine to form that is mass by charge ratio.


When it reaches the detector it strikes with a metal wall while electrons jump out by neutralizing the positive charge. This jumping of an electron leaves a gap behind an electron shuffle to fill this gap flow of electrons can be measured and amplified as an electric current.

For detection of the lighter electrons, the field has to be reduced whereas for heavier ones it has to be increased.

Mass Analyzer

Magnetic sector type instruments are made up of magnetic and electric field that bends the beam of ions traveling at very high energy. Once upon a time, they are the most favored analyzer for their high resolution whereas low sensitivity when scanning.

Quadrupole Mass Spectrometer

It is the most common mass spectrometer because of its simplicity, sensitivity, and quick scan speed.

It has four rods and has a combination of ratio frequency and direct current. The combination is selected to allow a specific mass by charge ratio. The first two parts are the ion selector and the third one is the mass analyzer.

Ion Trap Mass Spectrometer

It stores and manipulates ions. More sensitive than the quadrupole and full scan speed. The limitation is that, the fragmentation is not that extensive in comparison to instruments having a two-quadrupole at the front end.

Time of Flight (TOF)

It is relatively simple to mass spectroscopy because they just measure the time taken by ion to travel a specific distance to with specific energy. Larger ions take a longer time. These instruments are sensitive and fast. Resolution is very high by increasing path length.

Fourier Transform Mass Spectrometry (Fourier Transform Ion Cyclotron Resonance Spectrometry) (FTMS)

It usually refers to Fourier transform ion cyclotron motion caused by the ion in the magnetic field. The frequency of that motion is dependent upon the mass by the charge of the ion. It has high resolution and mass accuracy. Resolution dependent upon scan time and magnetic field.

Molecular Ion Peak

When the vaporized organic sample passes through the ionization chamber of mass spectroscopy bombarded with a beam of electrons having enough energy to knock out the electron from the molecule making it a positive molecular ion which is often given with a sample. This remains unstable and breaks into small fragments.


• It helps in toxicological analysis.
• Mass spectroscopy helps in examination of trace evidence.
• It helps in arson investigations.
• Mass spectroscopy is extremely useful in examination of explosive residue.