Introduction to Proteomics: Tools for the New Biology

This is an introductory, single-authored introduction to proteomics, which is currently the hottest thing in the biological sciences as it enable scientists to study the protein complement of the genome. It refers to studying the functions of many proteins at one time, as opposed to how research was conducted in the mid-90's where the technology did not enable the study of the entire protein system. From this, one is able to develop a systematic overview of the way a genome functions and the role it plays in health and disease. Daniel C. Liebler masterfully introduces the science of proteomics by spelling out the basics of how one analyzes proteins and proteomes, and just how these approaches are then employed to investigate their roles in living systems. He explains the key concepts of proteomics, how the analytical instrumentation works, what data mining and other softeware tools do, and how these tools can be integrated to study proteomes. Also discussed are how protein and peptide separation techniques are applied in proteomics, how mass spectrometry is used to identify proteins, and how data analysis software enables protein identification and the mapping of modifications. In addition, there are proteomic approaches for analyzing differential protein expression, characterising proteomic diversity, and dissecting protein-protein interactions and networks.

Table of Contents:
I. Proteomics and the Proteome.- 1. Proteomics and the New Biology.- 2. The Proteome.- II. Tools of Proteomics.- 3. Overview of Analytical Proteomics.- 4. Analytical Protein and Peptide Separations.- 5. Protein Digestion Techniques.- 6. Mass Spectrometers for Protein and Peptide Analysis.- 7. Protein Identification by Peptide Mass Fingerprinting.- 8. Peptide Sequence Analysis by Tandem Mass Spectrometry.- 9. Protein Identification with Tandem Mass Spectrometry Data.- 10. SALSA: An Algorithm for Mining Specific Features of Tandem MS Data.- III. Applications of Proteomics.- 11. Mining Proteomes.- 12. Protein Expression Profiling.- 13. Identifying Protein-Protein Interactions and Protein Complexes.- 14. Mapping Protein Modifications.- 15. New Directions in Proteomics.

Review :
Professor Daniel Liebler presents a tutorial on mass spectrometry and its use in proteomics. The basics of mass spectrometers and ionization techniques are described, which is important to ascertain what type of mass spectrometer is most particular for a particular study. The ability to use mass spectrometry data to search databases is an important advance for the non-specialist, because it no longer requires the development of the skills to interpret mass spectra. A basic understanding of the fundamental of the search algorithms and their limitations is described in the book. Finally, applications of mass spectrometry to proteomics are described. This book provides and excellent introduction and overview of proteomics for the graduate student or for any biologist interested in understanding the basics of this rapidly evolving area. - From the foreword by John R. Yates, III there is a wonderful description of mass spectrometry of peptides, both simple, accurate, up-to-date and very pleasant to read. This book can be recommended for people needing an update in mass spectrometry in proteomics - Proteomics a tutorial of mass spectrometry for the biological sciences in general and more specifically for the field of proteomics, Although designated as a book for beginners, it will almost certainly find a wider audience. In particular, both academics and researchers working in associated fields with a need to hone their knowledge skills will find much to interest them in this well written book. - Chromatographia ...wonderful description of mass spectrometry of peptides, both simple, accurate, up-to-date and very pleasant to read. - Proteomics As such, it is an excellent introduction to the principles and concepts of global protein analysis and because the book is a paperback represents good value for money. Also, the book wold serve as a useful introduction to more experienced researchers wishing to learn about less well-known aspects of proteomics, particularly the sections on studying protein-protein interactions and protein modifications. The real quality of the book is that, despite having to describe some very complicated techniques and principles, it is easy to read and understand is well-written...the layout of the book is excellent and the short, titled sections of text mean that the book is easy to read and flows in a logical pattern. In summary, this book represents an excellent, value for money introduction to proteomics. The author has very successfully managed to explain the complex concepts and principles in a fashion that is easy to read and understand. The book would be an invaluable source of reference for any researcher wishing to embark on a project involving proteomics. - Natural Products Reports