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Figure 2. Protocol for protein identification with the use of mass spectral data from a MALDI-TOF mass spectrometer. (A) The protein spot of interest on a 2-DE gel (indicated by arrow) is excised either by hand or by a robotic sampler. (B) Tryptic digestion of protein spot and transfer of peptides to a MALDI-TOF target plate. (C) Ions are generated by the firing of a laser at a target plate and a fingerprint spectrum of the relative masses of peptide ions calculated based on the time difference between the laser firing and the arrival of the ions at a detector. (D) The protein is identified by access to a database containing a theoretical digest of proteins from either the organism of interest or one that is closely related. The theoretical masses are compared with the experimentally observed masses, with accurate protein identification dependent on the total percentage of the sequence covered by the matching peptides and the size of the original protein.
