The method was developed in 1993 by several groups independently. The peptide masses are compared to either a database maldi mass spectrometry pdf known protein sequences or even the genome. This is achieved by using computer programs that translate the known genome of the organism into proteins, then theoretically cut the proteins into peptides, and calculate the absolute masses of the peptides from each protein.
They then compare the masses of the peptides of the unknown protein to the theoretical peptide masses of each protein encoded in the genome. The results are statistically analyzed to find the best match. The advantage of this method is that only the masses of the peptides have to be known. A disadvantage is that the protein sequence has to be present in the database of interest.
Additionally most PMF algorithms assume that the peptides come from a single protein. The presence of a mixture can significantly complicate the analysis and potentially compromise the results. Typical for the PMF based protein identification is the requirement for an isolated protein. MS analysis of gel spot eluates.
Disulfide bridges in proteins are reduced and cysteine amino acids are carbamidomethylated chemically or acrylamidated during the gel electrophoresis. Matrix and peptide molecules co-crystallize on the MALDI target and are ready to be analyzed. There is one predominantly MALDI-MS sample preparation technique, namely dried droplet technique. The target is inserted into the vacuum chamber of the mass spectrometer and the desorption and ionisation of the polypeptide fragments is initiated by a pulsed laser beam which transfers high amounts of energy into the matrix molecules. The energy transfer is sufficient to promote the ionisation and transition of matrix molecules and peptides from the solid phase into the gas phase.
The ions are accelerated in the electric field of the mass spectrometer and fly towards an ion detector where their arrival is detected as an electric signal. The mass spectrometric analysis produces a list of molecular weights of the fragments which is often called a peak list. The mass of these peptide fragments is then calculated and compared to the peak list of measured peptide masses. The results are statistically analyzed and possible matches are returned in a results table. Rapid identification of proteins by peptide-mass fingerprinting”.