Matrix-assisted laser desorption ionization a laser beam is fired at the crystals in the MALDI spot. The matrix absorbs the laser energy and it is thought that primarily the matrix is ionized by this event. The matrix is then thought to transfer part of its charge to the sample molecules , thus ionizing them while still protecting them from the disruptive energy of the laser. Ions observed after this process consist of a neutral molecule [M] and an added or removed ion. Together, they form a quasimolecular ion, for example [M+H]+ in the case of an added proton, [M+Na]+ in the case of an added sodium ion, or [M-H]- in the case of a removed proton.
The matrix consists of crystallized molecules, of which the two most commonly used are 3,5-dimethoxy-4-hydroxycinnamic acid, α-cyano-4-hydroxy Cinnamic acid A solution of one of these molecules is made, often in a mixture of highly purified water and an organic solvent such as acetonitrile or ethanol.
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