Mass Spectrometry of Proteins (Proteomics)

The completion of genome projects represents a pinnacle of human enterprise in the biosciences. The orchestration of technologies in mass spectrometry, genome science, and computer sciences has created a new branch of molecular bioscience called proteomics. A proteomics approach to the study of protein expression and posttranslational modification does not require foreknowledge of the identity of target proteins. A proteomic investigation begins with the discovery of unidentified proteins of interest under well-defined physiological conditions. The approach involves (1) protein display by 2-D gel electrophoresis or other separation technique; (2) determination of protein entities of interest; (3) peptide mass fingerprinting (PMF); and (4) genome/proteome database search. The methodology of the proteomics approach is characterized neither by deduction nor by induction in the traditional sense, but is a clear example of what C. S. Peirce described as abductive inference a century ago. The investigation of molecular and cellular events is often intractable to deductive and inductive methods due to its extreme complexity and nonlinearity. Proteomics is a powerful tool to study complex biological systems because of its characteristics: (1) no a priori knowledge of the protein's identity is required to initiate a project; and (2) a holistic approach is possible for investigation. It is expected that proteomics will substantially contribute to the future development of molecular medicine.