Introduction to mass spectrometry (MS)

Introduction to mass spectrometry

Mass spectrometers use the difference in mass-to-charge ratio (m/e) of ionized atoms or molecules to separate them from each other. Mass spectrometry is therefore useful for quantitation of atoms or molecules and also for determining chemical and structural information about molecules. Molecules have distinctive fragmentation patterns that provide structural information to identify structural components.

All commonly used mass analyzers use electric and magnetic fields to apply a force on charged particles (ions). The relationship between force, mass, and the applied fields can be summarized in Newton's second law and the Lorentz force law:

F = ma (Newton's second law)

F= e(E+ v x B) (Lorentz force law)


  • F is the force applied to the ion,
  • m is the mass of the ion,
  • a is the acceleration,
  • e is the ionic charge,
  • E is the electric field
  • v x B is the vector cross product of the ion velocity and the applied magnetic field

From Newton's second law, it is apparent that the force causes an acceleration that is mass-dependent, and the Lorentz force law tells us that the applied force is also dependent on the ionic charge. Therefore, it should be understood that mass spectrometers separate ions according to their mass-to-charge ratio (m/z) rather than by their mass alone.

The general operation of a mass spectrometer is:

  • create gas-phase ions
  • separate the ions in space or time based on their mass-to-charge ratio
  • measure the quantity of ions of each mass-to-charge ratio

The ion separation power of a mass spectrometer is described by the resolution R, which is usually defined as:

where m is the ion mass and ∆m is the difference in mass between two resolvable peaks in a mass spectrum.



In general a mass spectrometer consists of an ion source, a mass-selective analyzer, and an ion detector. The magnetic-sector, quadrupole, and time-of-flight designs also require extraction and acceleration ion optics to transfer ions from the source region into the mass analyzer. The details of mass analyzer designs are discussed in the individual documents listed below.

Basic descriptions of sample introduction/ionization and ion detection are discussed in separate documents on ionization methods and ion detectors, respectively.


Common mass analyzer designs:


Interpretation of mass spectras

The output of the mass spectrometer shows a plot of relative intensity vs the mass-to-charge ratio (m/e). The process of fragmentation follows simple and predictable chemical pathways and the ions which are formed will reflect the most stable cations and radical cations which that molecule can form.

An introduction in this field is given in a separate document.