Matrix-Assisted Laser Desorption/ Ionization Time-Of-Flight Mass Spectroscopy, briefly MALDI-TOF MS or MALDI, is a powerful technique to identify protein in biological samples. Usually, the proteins in the sample have been separated by one-dimensional or two-dimensional gel electrophoresis prior to MS analysis. After electrophoresis, the protein is cut from the gel, digested into peptide fragments and spotted to a metal target plate. The spotting is done in the presence of a suitable ‘matrix’, which mediates in the ionization of the peptide fragments. Inside the mass spectrometer, ionized peptides are volatilized, accelerated in an electric field and caught in a detector. The time of flight of the ion is directly dependent on the mass of the particular peptide fragment. In this way, the mixture of polypeptides derived from the digested protein gives a unique fingerprint of molecular masses. The spectrum is compared with polypeptide masses calculated from genomic data. The comparison and statistical analysis is done by a computer program, which scores the protein(s) that meet(s) the mass spectrum. The scoring is given together with the statistical significance.

The Nijmegen Proteomics Facility has the disposal of Bruker Biflex III MALDI-TOF MS. The machine is located at the Department of Microbiology at the Faculty of Science. The Department is happy to share the facility with other researchers. We also offer scientific and technical support.