Proteomics defined

Proteomics is the study of the proteome—defined as the total set of proteins expressed in a given cell type at a given time [27]. Tremendous progress has been made in the past few years in generating large-scale cellular protein profiles, organelle composition, protein activity patterns, and datasets for protein-protein interactions. 

The proteome defines the entire range of proteins in an organism, each a complimentary part of the machinery of life and the physiological components of metabolic... 

Structural genomics is the systematic effort to gain a complete structural description of a defined set of molecules, ultimately for an organism s entire proteome. Structural genomics projects apply X-ray crystallography and NMR spectroscopy in a high-throughput manner. 

The proteome has been defined as the entire protein complement expressed by a genome. Thus the field of proteomics involves the extensive study of the dynamic protein products of the genome and includes... 

Several biochemical events occur posttranscriptionally that define the response of cells to stimuli. For instance, alternative splicing, posttrans-lational modifications, regulation of enzyme activities, distribution of metabolites between cellular compartments, necessitate analysis at the level of the proteome and the metabolome. 

This chapter has reviewed the application of ROA to studies of unfolded proteins, an area of much current interest central to fundamental protein science and also to practical problems in areas as diverse as medicine and food science. Because the many discrete structure-sensitive bands present in protein ROA spectra, the technique provides a fresh perspective on the structure and behavior of unfolded proteins, and of unfolded sequences in proteins such as A-gliadin and prions which contain distinct structured and unstructured domains. It also provides new insight into the complexity of order in molten globule and reduced protein states, and of the more mobile sequences in fully folded proteins such as /1-lactoglobulin. With the promise of commercial ROA instruments becoming available in the near future, ROA should find many applications in protein science. Since many gene sequences code for natively unfolded proteins in addition to those coding for proteins with well-defined tertiary folds, both of which are equally accessible to ROA studies, ROA should find wide application in structural proteomics. 

It has been argued that in a typical 2DLC proteomic experiment, with only a limited number of fractions submitted for analysis in the second LC dimension, chromatographic peak capacity is less than 1000. This value is considerably lower than the expected sample complexity. Additional resolution is offered by MS, which represents another separation dimension. With the peak capacity defined as the number of MS/MS scans (peptide identifications) accomplished within the LC analysis time, the MS-derived peak capacity was estimated to be in an order of tens of thousands. While the MS peak capacity is virtually independent of LC separation performance, the complexity of the sample entering the MS instrument still defines the quality of MS/MS data acquisition. The primary goal of 2DLC separation is to reduce the complexity of the sample (and concentrate it, if possible) to a level acceptable for MS/MS analysis. What is the acceptable level of complexity to maintain the reliability and the repeatability of DDA experiments remains to be seen. 

Celis JE et al. Proteomics and immuno-histochemistry define some of the steps involved in the squamous differentiation of the bladder transitional epithelium a novel strategy for identifying metaplastic lesions. Cancer Res 1999 59 3003-3009. 

Ostergaard M et al. Proteome profiling of bladder squamous cell carcinomas identification of markers that define their degree of differentiation. Cancer Res 1997 57 4111 117. 

Many diseases are characterized by the expression of specific proteins1 in some cases, malignant cells yield unique protein profiles when total cellular protein extracts are analyzed by proteomic methods such as two-dimensional gel electrophoresis or matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS).2 High-throughput proteomic studies may be useful to differentiate normal cells from cancer cells, to identify and define the use of biomarkers for specific cancers, and to characterize the clinical course of disease. Proteomics can also be used to isolate and characterize potential drug targets and to evaluate the efficacy of treatments. 

However, IHC as a practical method continues to evolve with increasing demands for standardization, and for true quantification of protein analytes by weight, in the context of their cellular microenvironment. Further studies combining proteomics by mass spectrometry and IHC are likely to lead to the refinement of both methods in the analysis of FFPE tissues. The end result may be the creation of a broader field that defines and quantifies protein expression at a cellular level, incorporating the advantages of the wide spectrum of proteins demonstrable by mass spectrometry and the precise localization offered by IHC. 

Protein (as pure as possible) is specifically cleaved with a protease under defined conditions. Thus the mixture of peptides, specific for the given protein, is produced. In classical proteomic approach this step is generally preceded by separation of individual proteins, usually by two-dimensional electrophoresis. 

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