Matrix-assisted laser desorption/ionization (MALDI)- Time of flight (TOF) is a kind of mass spectrometer  and allows the analysis of biomolecules (biopolymers such as DNAproteinspeptides and sugars) and large organic molecules such as polymersdendrimers and other macromolecules.

Here, molecules are ionized and rushed in to the TOF part and according to their time of flight, peptides or other biomolecules are detected in the detector part. The detection of these ions depend on the mass and the ions ratio (m/z).

In our unit α-Cyano-4-hydroxycinnamic acid (CHCA), sinapinic acid (SA) and 2,5-dihydroxybenzoic acid  are used as ionization matrices.  The choice of matrix can be changed according to the sample type or its handling process. Our unit can provide consultancy while choosing the matrix. After detection of ions, protein identification is  performed  by peptide mass finger printing (PMF) and the masses are compared to either a database containing  known protein sequences or even the genome. This is achieved by using special softwares such as Mascot, Plgs and translate the known genome of the organism into proteins, then theoretically cut the proteins into peptides (with the protease sides that we use such as trypsin-Chymotrypsin), and calculate the absolute masses of the peptides from each protein.  Protein identification is performed by comparing the masses of the peptides of the unknown proteins to the theoretical peptide masses of each protein encoded in the genome.