Proteins purified by HPLC or excised from a mono or bi-dimensional electrophoresis gel can be digested in vitro by proteolytic enzymes, such as trypsin, yielding a mixture of peptides generated on the basis of the presence of Arginine and Lysine residues in the original protein sequence. The peptide mixture is then analysed by MALDI-TOF mass spectrometry which gives the accurate molecular weight of some or most of the peptides (mass spectrometry fingerprinting). The comparison of the experimental molecular weights with those generated by virtual computer theoretical trypsin digestions of the protein sequences present in public databases, allows us to determine the nature of the protein sample and to precisely identify the protein target.
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