Matrix-assisted laser desorption ionization 

Matrix-Assisted Laser Desorption Ionization or MALDI is a soft ionization technique, allowing, amongst others, to ionise biomolecules (biopolymers like proteins, peptides, sugarchains,...) which tend to be more fragile and quickly lose structure when ionised by more convential ionisation methods.

The principle is simple. The ionization is triggered by a laser beam (normally a nitrogen-laser), the problem is, really, that a direct laser beam on the biomolecule (for instance, a protein) would destroy it. That is where the matrix comes in play.

The matrix consists out of crystallized biomolecules, of which 3 are most common: 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid ), a-cyano-4-hydroxycinnamic acid (alpha-matrix) or 2,5-dihydroxybenzoic acid (DHB ). A solution of one of these molecules is made, in a mixture of highly purified water and another organic compound (normally acetonitrile (ACN) or ethanol). Normally also some trifluoracetate (TFA) is added.

A good example of a matrix-solution would be: 20mg/ml sinapinic acid in ACN:water:TFA (50:50:0.1).

The matrix-solution is then brought onto the protein-sample which you wish to investigate. The organic compound ACN allows for the hydrophobic proteins in the sample to dissolve into the solution, while the water allows for water-soluble (hydrophilic) proteins to do the same. The solvents vaporize, leaving only the recrystallized matrix, but now with proteins spread throughout the crystals.

The laser is then fired onto the crystals. These will absorb the laser energy, becoming ionized. They will then transfer part of their charge to the proteins, thus ionizing them while still protecting them from the disrubitve energy of the laser.

The proteins are then ready to be inserted in a mass spectrometer. A common type of a MALDI spectrometer is the MALDI-TOF, with TOF standing for Time-of-flight.