Introduction to Proteomics: Tools for the New Biology.

By Daniel C. Liebler

Totowa, NJ:Humana Press, Inc., 2002. 198 pp. ISBN: 0 89603-991-9, $49.50 cloth. ISBN: 0-89603-992-7, $29.50 paper

The so-called New Biology is really a fresh approach to studying living systems by taking one step back and studying entire sets of biomolecules and their life cycles and interactions, rather than studying each biomolecule individually. In Introduction to groteomics: Tools for the New Biology, Daniel Liebler, a leading innovator in this field, provides an excellent introduction to techniques used in this field. This book will serve as an introductory text for biotechnology curricula, for graduate students in biomedical research, and for biologically oriented research scientists considering incorporating New Biology approaches into their research.

In this book, Liebler explains some fundamental aspects of analytic chemistry and mass spectrometry in simple, straightforward terms, using everyday analogies and simple declarative language. He makes effective use of simple diagrams to describe molecular-level interactions. The book is divided into discussions of what proteomics is, what tools it uses, and, finally, how it is applied to answer questions in biological research.

Liebler points out that in the almost universally applicable field of proteomics, there are really only a few types of experiments: analysis of intact proteins using very high-resolution mass spectrometry (MS), comparative analysis of peptide mass fingerprints and genomic databases, peptide sequence analysis of 5-20 residues followed by genome mining, and de novo peptide sequencing with post-translational modification determination. This simple group of approaches is applied to a large group of biological problems, including study of gene expression, protein processing and trafficking, and especially the study of interactions with other proteins, with nucleic acids, and with the host of small molecules involved in intermediary metabolism.

As the field of proteomics develops, parallel and competing approaches have developed, and each has its advocates. As with all practitioners of this art and science, Liebler has his preferences, and he provides more extensive treatment to certain of these areas. A particular strength of the book lies in the detailed discussion of the integrated use of multidimensional chromatography, ion-trap MS-MS, and his data mining approach using the Scoring Algorithm for Spectral Analysis (SALSA).

Despite these preferences, for each of the competing techniques e.g., chromatography vs. electrophoresis, fingerprinting vs. sequencing, post hoc data mining vs. data-dependent acquisition) Liebler lists strengths and weaknesses, helping to guide a neophyte user's choices. The presentation, taken as a whole, leads one to conclude that the many competing technologies are in fact complementary approaches and that all of them will continue to be useful for certain areas of proteomics.

The book is not comprehensive, nor could it be in such a dynamic field. It is not a cookbook. The underlying theory and strategies are explained effectively, but there is no attempt to provide preferred vendors, protocols, recipes, or operating procedures. Some exciting areas of development in structural analysis applications--for example, study of intact proteins using high-resolution fast Fourier transform mass spectrometry--are not addressed. But this book is what it purports to be, an excellent introduction to the practice of proteomics. Directors of core mass spectrometry or proteomics facilities would be wise to recommend this book both to students and to collaborators who are biological and biomedical research scientists just beginning to use these approaches.

William M. Pierce, Jr., is professor of pharmacology and toxicology, professor of chemistry, and director of the Biomolecular Mass Spectrometry Laboratory in the University of Louisville's School of Medicine, and College of Arts and Sciences.