Mass spectrometry only works with ions, not with neutral molecules. That means a neutral molecules must become charged in order to do this experiment. It is common to generate a cation from the molecule by removing one electron. The electron is knocked off the molecule in a collision. The collision can be caused in two different ways:
- The molecule can be sent through a stream of high-energy electrons. This method is called electron ionization.
- The molecule is sent through a stream of small molecules, such as ammonia or methane. This method is called chemical ionization.
- Electron ionization frequently results in the molecule falling to pieces because of the high energy of the electrons.
- Chemical ionization results in a "softer" collision because momentum can be dissipated through various bonds in both colliding molecules. Chemical ionization results in less fragmentation of the target molecule.
- However, after chemical ionization, the ionizing molecule sometimes sticks to the target molecule, leading to a greater "molecular" mass. For example, if ammonia is used for ionization, an extra mass may be observed at 17 amu higher than expected.
The reason the x-axis on a mass spectrum is labeled m/z (mass-to-charge ratio) is to acknowledge that there are really two factors contributing to the experiment.