Matrix in mass spectrometer

The function of the matrix is adsorborption of energy from laser pulse, and then transfer to sample“thereby causing desorption of the analyte molecules in an expanding plume, to ionize the desorbed analyte molecules and to prevent aggregation of the analyte molecules”(2). The matrix molecules for MALDI are chosen on the basis on fulfillment of requirement that matrix molecules must be able to absorb ultraviolet wavelength of usually 237nm, low volatility and ability to transfer protons to the sample molecules. For proteins samples typical MALDI matrix consist of cinnamic acid and hydroxylated benzoic acid derivatives.

2,5-dihydroxybenzoic acid is more tolerant to the sample contaminants because it excludes them during crystallization process(3). The use of specially prepared thin matrix layers uses fast evaporation setup, which not only improves the sensitivity and resolution, but also allows the samples to be extensively washed, removing salts and detergents. Since the sensitivity depends on the concentration of the sample on the target plate, samples can be concentrated using PR-HPLC or bead-peptide concentration. In bead-peptide concentration RP-chromatographic beads are added to the proteins or peptide samples, and these samples preferentially bind to the beads through hydrophobic interactions while the contaminants like salts and chaotrophes do not. After a short incubation, the peptide-bead solution is harvested using pellets from a centrifugation, and dried in speed vacuum concentrator. In both cases, highly concentrated pellets of peptide-bound beads are obtained, which can be transferred to MALDI and left to dry. Because the beads are hydrophobic in nature, they form a cluster in highly concentrated spot (<1mm^2) on MALDI target plate after drying. Peptides elute on the target plate by a small volume of aqueous/organic MALDI-matrix solution and become incorporated into the growing matrix crystals at the same time. This process allows 10 to 100 fmol to be enough to be loaded on to the gels.