Collision induced fragmentation

Fragmentation can be carried out to some extent even in a simple single quadrupole instrument. This is done simply by accelerating the ions into the detector through the first stages of the instrument a little too fast. "Too fast" means fast enough that when they collide with molecules of air, they strike with enough energy to break a bond, and smaller daughter ions are produced.

Source ionization is a messy thing, and it can be hard to work out which parent gave rise to which daughter. Ion traps (and triple quadrupoles) provide a much neater solution.

In the ion trap, a particular parent ion can be trapped, and then fragmented after first expelling all the other, unwanted ions. There are therefore three stages:

The scanning of fragments can be achieved in exactly the same way as the scanning of a full trap in normal full MS mode (see how an ion trap works).

Expulsion of unwanted ions is achieved by resonance. All the ions are going round in little orbits. The rates (revolutions per minute!) that the ions go round vary with mass, and are all slower than the normal AC frequency applied to the trap. The frequencies of the ions' orbits are called their secular frequencies, and large ions go round slowest.

By applying a mixed wave-form to the end-caps, containing all frequencies up to the secular frequency of the ion you want to trap, and all frequencies above it, but NOT the actual frequency of the ion you want, all the others can be pushed out.

Having trapped the ion that is interesting, and got rid of the rest, it must be fragmented. This can be done by applying just a little of its secular frequency - enough to make it orbit more violently at higher speed, but not enough that it actually leaves the trap. In this new orbit it will strike the Helium dampening gas at increased energy, enough to break bonds.

Note that as soon as the ion has broken, its daughter fragments have lower masses. If you are unlucky, they might be so low that they cease to be stable in the trap, and are lost. More often they remain in the trap, but are no longer excited by the frequency across the end-caps. Therefore ion-traps tend to make few fragments compared to other collision induced systems (e.g. triple quad). But this doesn't matter: in an ion trap you can always collect the daughter, and carry out another round of fragmentation...