The Evolution from Protein Chemistry to Proteomics Basic Science to Clinical Application potx

[...]... fragments, the limited stability of these targets and the high variance of on/off rates Proteomics describes an experimental approach to the study of complex protein mixtures such as described by Dutt and Lee20 and Dreger21 and we will focus on the application of solution protein chemistry to proteomics and the limited success in some areas together with the challenges of reducing the research to practice... modifications of proteins separate from translational processing as such modifications are of major interest to investigators using proteomics to study toxicology and environmental health The reader is directed to several reviews for experimental detail1–3 on the specific chemical modification of proteins 23 24 The Evolution from Protein Chemistry to Proteomics SPECIFIC CHEMICAL MODIFICATION OF PROTEINS This... systems The application of chemical techniques to problems in biology — the author has no idea how this differs from biochemistry or, perhaps more relevant, biological chemistry Use of chemical modification to identify enzymes in the proteome The use of small molecules as affinity materials for the discovery of specific binding proteins in the proteome Term TABLE 1.1 Useful Definitions 4 The Evolution from Protein. .. involved in the cross-linking of collagen.5 The reactivity of a functional group in a protein is largely dependent upon two factors The first is the nucleophilicity of the amino acid residue and the second is the accessibility of the functional group to the chemical reagent The nucleophilicity of a functional group is in turn a function of the inherent chemistry of the functional group and the environment... the mass proportional to the square of the time; converted to m/z by calibration with standards Analysis of the intact unknown proteins by mass spectrometry; occasionally used to describe the analysis of cyanogen bromide peptides A technology which analyzes proteins on a single cell level; study of the toponome The total RNA transcripts produced by a genome; the complete set of RNA messages coded from. .. mass -to- charge ratios to ions based on their momentum, cyclotron frequency, time-of-flight or other parameters The total metabolites produced by the products of the genome The study of the metabolome The sum of all post-translational modifications of the proteome Global proteomics Glycome Glycomics Hypsochromic Immunomics Immunoproteomics Definition Term TABLE 1.1 Useful Definitions (Continued) 6 The Evolution. .. abnormalities The proteases and protease substrates of the proteome The use of algorithms to determine the relationship of multiple proteins as determined by mass spectrometric or liquid chromatographic analysis The use of proteomics to predict individual reaction to a drug or drugs; related to personalized medicine, theranostics, pharmacogenomics The physical manifestation of the genes of an organism; the collection... from the DNA within a cell Soft-ionization Structural proteomics Structural biology Structural genomics Surrogate marker Synovial proteome Systems biology a The distinction between peptide and protein can be arbitrary Top-down proteomics Topological proteomics Transcriptomics Time-of-flight Targeted proteomics Theranostics Definition Term TABLE 1.1 Useful Definitions (Continued) 8 The Evolution from Protein. .. have focused on the identification of biomarkers for the development of diagnostics are discussed in the chapter on clinical proteomics DIVISION OF ACTIVITIES IN PROTEOMICS ANALYTICAL PROTEOMICS In considering the vast literature on proteomics, three general types of activities appear that are closely related to each other The first is the elucidation of the proteome by analytical biochemistry, including... opportunity to look at pathways (pathway proteomics) rather than individual proteins.94 The techniques required for the study of expression proteomics are discussed in the chapter on chemical modification and aspects of application in the chapter on chemical proteomics BIOMARKER IDENTIFICATION The third general area is biomarker identification, where the protein composition in tissue samples from certain .