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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