Friday, 6 September 2013

Proteomics

Proteomics is an interdisciplinary science that includes biology, bioinformatics, and protein chemistry. The purpose of this book is to provide the reader with an overview of the types of questions being addressed in proteomics studies and the technologies used to address those questions. The first chapter is a concise outline of the field as it presently stands. The second chapter provides an overview of the use of 2D-gel electrophoresis and mass spectrometry to identify proteins, as well as post-translational modifications of proteins, on a genome-wide scale. The chapter also includes an assessment of the limitations of this approach and outlines new developments in mass spectrometry that will advance future research. Chapter three describes the use of mass spectrometry to characterize the changes in protein expression profiles in different cell types or in the same cell type under different experimental conditions. The fourth chapter outlines high-throughput recombinant DNA cloning methods used to systematically clone all of the open reading frames of an organism into plasmid vectors for large-scale protein expression and functional studies such as protein-protein interactions with the two-hybrid system.

An important and growing aspect of proteomics is the attempt to generate protein-protein interaction maps for an entire genome. This information is crucial to an understanding of how genes work in concert to generate a working cell. This information, in conjunction with knowledge of transcriptional regulation obtained from microarray experiments, will provide insights into gene function. Chapter five details the experimental approaches used to generate protein-protein interaction maps including the yeast two-hybrid system, mass spectrometry and phage display. Chapter six is a summary of several computational approaches to identify protein interaction networks. Chapter seven describes attempts to create protein microarrays analogous to the DNA chips used to study RNA levels. Protein arrays hold the promise of fast, sensitive protein-protein and protein-ligand interaction mapping on a genome-wide scale. In addition, protein arrays will greatly facilitate drug discovery by allowing the rapid determination of protein targets for a prospective drug. Finally, this chapter covers efforts at determining the function of genes by the activity of the protein products. This involves the large scale cloning, expression and purification of all of the proteins of an organism. This approach has been termed biochemical genomics. Finally, chapter eight describes current limitations and possible future directions for proteomics research.

It is hoped that this book will provide the basis for understanding the field of proteomics. It is not intended to cover every aspect of the field in encyclopedic style but rather to serve as a starting point for more advanced study. Because proteomics is a young and rapidly evolving field, the best approach is to gain a general understanding of the questions and technologies involved and then pursue to the primary literature for detailed information on the latest developments.



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