A technique that separates molecules based on mass (and charge). The most commonly used method of mass spectrometry is Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) spectrometry. The way this technique works is to immobilize your sample (can be either a mixture of various substances, or a single substance) on a solid matrix. A laser then strikes this matrix, and the energy from the laser ionizes the sample (imparting a charge to some of the molecules). An electric field is applied, and the charged molecules all fly off towards the detector, a short distance away. Molecules with higher mass, or less charge, will accelerate more slowly, and hit the detector later. Usually the same molecule will exist with several different charges, +1, +2, +3, etc. This gives good redundancy for double checking results, and provides very accurate molecular weights of compounds. With modern mass-spec systems it is possible to measure molecules up to 1,000,000 Daltons, or as small as 20 Daltons, with an error of about .01%.

One of the coolest new uses for mass spectrometry is in the field of protein identification.

One uses a tandem mass spectrometer, in which a mixture containing proteins is first separated (by mass/charge) by the first mass spectrometer. Then, this protein/peptide is fragmented, and individual fragments are detected. This gives you a spectrum that is chracteristic for each unique peptide.

The spectrum alone could be used to arrive at a peptide sequence via brute-force techniques, but the clever bit uses the public DNA/protein database known as Genbank. By using a program to generate theoretical mass/charge spectrums for each peptide in the database, one can match up the measured spectrum with an entry in the database.

I know it works, I got data from it that's going into my thesis.

The technique of mass spectrometry is now well established as a means for obtaining the formulae and structures of molecules. It enables many sophisticated structural problems to be solved rapidly, even when only minute quantities of material are available.

The principle of the method is to obtain a positively charged ion characteristic of the substance under investigation, and then to determine the mass of this ion using an approach closely related to that employed by J.J. Thomson for measuring the charge-to-mass ratio (z/m) for electrons. The procedure involves the use of electric and magnetic fields to deflect the charged particles.

Thomson used a magnetic field to deflect a beam of positive ions, obtained by the ionization of neon atoms. Close examination of the trace produced by the positive ions as they impinged on a detector demonstrated that there were two different types of ion, characterized as those from the two neon isotopes (20Ne and 22Ne), which differ in mass because of the different numbers of neutrons in their nuclei.

A mass spectrometer works as follows. A very small amount of the vapour of the substance to be studied (obtained, for example, by heating the sample) is introduced into an ionization chamber at very low pressure (about 10-4 Nm-2). The vapour is then bombarded with high-energy electrons, and the collision between an electron and a molecule M (or atom) causes an electron to be ejected, leaving a positively charged ion (M+). The ions are then attracted by an applied electrostatic potential and are hence accelerated toward a negative plate. The ions pass through a slit in the plate and into a magnetic field – the positive ions then become deflected by an amount which depends on their mass (m) and their charge (z). The lighter the ion and the greater the charge, the greater will be the deflection.

The derivation of the exact relationship is as follows: for an acceleration potential V the potential energy of an ion, or charge z, generated in an ion chamber is zV. The ion is accelerated through the slit, and in this process its potential energy zV is completely converted to kinetic energy ½ mv2, where m and v are the mass and velocity respectively, of the ion (eqn 1). When the positive ion passes into the magnetic field (of magnetic flux density B) it experiences a force at right angles both to the direction of motion and to the field direction. The magnitude of this force is Bzv. The positive ion is now constrained to move in a circle of radius R, as given in equation 2.

Equation 1: zV=(mv2)/2

Equation 2: BzV=(mv2)/R

Combination of these equations leads to the important expression linking m, z, B, R and V (eqn 3). This equation shows that for an ion of given mass (m) and charge (z) the radius of the circle of motion (R) is determined by B and V, i.e. the magnitudes of the magnetic and electric fields. In practice, R remains fixed by the geometry of the apparatus and the position of the detector. It can then be seen that if V is kept constant and B is varied, equation 3 will be satisfied for ions of different m/z for different values of B. The value of B needed to get a particular type of ion to be deflected to the recorder is a measure of the m/z for that ion.

Equation 3: m/z=(B2R2)/(2V)

Most positive ions generated will have lost just one electron and they will therefore have the same charge. This means that, as B is varied, ions of different mass will arrive at the detector and a spectrum of the masses of the various ions concerned can be plotted.

The setup described is an example of a relatively early mass spectrometer that achieves a fairly low resolution (i.e. separation of two fairly similar masses such as the neon isotopes). Many more modern mass spectrometers are designed with an extra focusing system which enables an increased resolution to be obtained. As before, a narrow beam of positive ions with a small but finite range of kinetic energies is produced: this spread of energies must be reduced for more precise work so that equation 3 is strictly applicable. This is achieved by passing the ions through an electric field (an electrostatic analyser) which deflects the ions according to their kinetic energies. Then only one small component of the resulting beam, with a well-defined kinetic energy, is passed into the magnetic field for the focusing of ions of given m/z values. As before a scan of mass is obtained by varying B (although in certain circumstances it is possible to obtain a more rapid scan by varying V, keeping B constant). An electron multiplier usually serves as a collector and detector of positive ions, and the arrival of ions gives rise to a signal. This procedure gives rise to a mass spectrum – effectively a plot of masses of the positive particles present against the relative number of ions of each mass. The scan is calibrated with a peak from a substance of known relative molar mass. The resulting spectrum can usually be obtained from less than a nanogram of material in a few seconds.


McMurray, J., Organic Chemistry (5th), 2000, Brooks-Cole

Jones, Jr., M., Organic Chemistry (2nd), 2000, W.W. Norton

Gilbert, B. and Duckett, S., Foundations of Spectroscopy, 2001, Oxford University Press

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