Mass spectrometry has become an important measurement tool in clinical chemistry, microbiology, toxicology and in the pharmaceutical world.  In order to measure the characteristics of individual molecules with a mass spectrometer, the molecules are ionized, accelerated, sorted according to their charge to mass ratio, and then detected.  The three essential components of a mass spectrometer are:

• The ion source:  It converts a sample to gas phase and ionizes the sample.
• The mass analyzer:  It sorts ions according to mass-to-charge ratio,
• The ion detector:  It produces an electrical signal proportional to the number of ions detected.

Ion Source:

Many ionization methods exist and the basic types are listed below.

Life scientists usually rely on two ionization methods: matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI).  MALDI is a solid phase technique that can analyze a digested protein sample from a 2-D polyacrylamide gel.  ESI, a liquid methodology, is compatible with high pressure liquid chromatography (HPLC) and capillary electrophoresis (CE).

The mass analyzer:

Different types of mass analyzers exist.  Here we concentrate on the magnetic sector analyzer.

Ions are accelerated by passing them through a potential difference V.  A voltage is placed across parallel plates and ion are injected at negligible speed into the area between the plates, near the plate that holds charge of the same sign as the ions.  The ions are repelled from that plate and accelerate towards the other plate at ground potential.  A small hole in that plate lets them pass out of the region between the plates.

When the ions enter the region between the plates, they have negligible kinetic energy and potential energy
U = qV.  
When the ions reach the ground plate, all the potential energy has been converted into kinetic energy
E_kin =  ½mv² = qV. 
The speed of the ions therefore is
v = (2qV/m)^½.

The ions now enter the mass separation stage.  This is simply a region with a uniform magnetic field perpendicular to the velocity of the ions.  The magnetic force F = qvB causes the ions to move on a circular path with radius
r = mv/qB.
Inserting v from above we find the radius of this path
r = (m/q)^½*(2V)^½/B,
Which we can solve for the charge to mass ration
q/m = 2V/(r²B²).

In the separator shown, the ions are detected after they have traveled half a circle in the mass separator.  All the ions enter the mass separator at the same point, but ions with different charge to mass ratios travel on paths with different radii and exit at different points.

The detector

Detectors may be position sensitive, recording the arrival of ions as well as their position on the detector, or they may be single channel and not be able to record position information.  A small slit is then put in front of the detector and a scanning technique is used.  The detector can be placed at a fixed position and the magnitude of the B field can be scanned, or the magnitude of B field can be fixed and the detector position can be scanned.

All these techniques can produce graphs of the number of ions detected versus the charge to mass ratio q/m.  Biological molecules produce several fragments when ionized.  Mass spectrometry does not yield the fragments' actual masses.  Rather, it determines their mass-to-charge ratio; if the ion charge is known, the mass can be calculated.  The fragments produce a mass spectrum that can be used to identify each molecule uniquely.

The major barrier to productive mass spectrometry analysis is not the instrumentation, but successful purification of bio-molecules suitable for analysis.  That is why sample preparation has become the most critical and challenging task in mass spectrometry analysis.  It involves purifying, storing, and recovering proteins, peptides, and other bio-molecules and removing such contaminating species as buffers, salts, and detergents prior to MS analysis.

Example spectrum: