Principles of Proteomics

Book Preface

Proteomics, a word in use for less than a decade, now describes a rapidly growing and maturing scientific discipline, and a burgeoning industry. Proteomics is the global analysis of proteins. It seeks to achieve what other large-scale enterprises in the life sciences cannot: a complete description of living cells in terms of all their functional components, brought about by the direct analysis of those components rather than the genes that encode them. The field of proteomics has grown rapidly in a short time, yet promises to provide more information about living systems than even the genomics revolution that started ten years before. The reason for this is the richness of proteomics data. Genes have sequences, but proteins have sequences, structures, biochemical and physiological functions, and their activities are influenced by chemical modification, localization within or without the cell, and perhaps most importantly of all, their interactions with other molecules. If genes are the instruction carriers, proteins are the molecules that execute those instructions. Genes are the instruments of change over evolutionary timescales, but proteins are the molecules that define which changes are accepted and which are discarded. It is from proteins that we shall learn how living cells and organisms are built and maintained, and how they fail when things go wrong.

As is the case for any emerging scientific field, proteomics makes a lot of sense to those performing large-scale protein analysis on a day-to-day basis, and much less sense to those looking in from the outside. Proteomics abounds with jargon and acronyms. New technologies and variations appear on what can seem to be a daily basis. It can be difficult to keep up, and even specialists in one area of proteomics sometimes have difficulties applying their knowledge in other specialized areas. It is my hope that this book will be useful to those who need a broad overview of proteomics and what it has to offer. It is not meant to provide expertise in any particular area: there are plenty of books on electrophoresis, mass spectrometry, bioinformatics etc. for the reader needing detailed treatment of particular technologies. However, this book pulls together disparate information concerning the different proteomics technologies and their applications, and presents them in what I hope is a simple and user-friendly manner. After a brief introductory chapter, the various proteomics technologies are discussed in more detail: two-dimensional gel electrophoresis, multidimensional liquid chromatography, mass spectrometry, sequence analysis, structural analysis, methods for studying protein interactions, modifications, localization and function. Protein chips, an emerging and promising recent addition to the proteomics armory, are described in the penultimate chapter. The final chapter presents a few examples of how proteomics is being applied, particularly in the medical and pharmaceutical fields. Again, this is not intended to be comprehensive coverage, but is provided so the reader has an overview of the scope of proteomics and its potential. At the end of each chapter is a short bibliography, containing some classic papers and useful reviews for those wanting to delve deeper into the subject. I have assumed that the reader has a working knowledge of molecular biology and biochemistry.

This book would not have been possible without the help and support of many people, not least the team at Garland/BIOS for their patience, persistence and optimism in the face of tight deadlines. I’d like to thank the many friends and colleagues who offered opinions on the individual chapters and pointed out potential errors or omissions, and in particular, I would like to thank all at the Fraunhofer Institute of Molecular Biology and