Briefings in Bioinformatics Advance Access originally published online on June 8, 2007
Briefings in Bioinformatics 2007 8(6):467-468; doi:10.1093/bib/bbm021
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Book Review |
Proteomics for Biological Discovery.
Edited by Timothy D. Veenstra and John R. Yates III
Proteomics for Biological Discovery.
Edited by Timothy D. Veenstra and John R. Yates III
John-Wiley & Sons, Hoboken, New Jersey, USA; 2006;
ISBN: 978-0-471-16005-2; Paperback/Hardback; 326 pp.; £41.50
‘Proteomics for Biological Discovery’ edited by Timothy D. Veenstra and John R. Yates III (342 pages, John-Wiley & Sons, publishers), defines the modern analytical challenges of proteomics in terms of quantification, detection and accuracy for biomedical research. The logic and possibly the elegance of this text comes from the way that the reader is able to converse with more than two dozen experts on a nearly complete collection of separation, automation and bioinformatics techniques required for quantitative and functional proteomic analysis. The book is divided into three parts: Part I is on the fundamentals of protein separations and mass spectrometry, Part II is on functional proteomic analysis and Part III discusses new methods that are at the frontier of the proteomics field. All of these methods are heavily dependent upon bioinformatics and/or computational modeling of protein sequence and structure.
The current practice of proteomics, though rapidly advancing into new methodologies, remains highly dependent upon mass spectrometry, and this text includes in Part I a clean description of mass spectrometric instrumentation, peptide fragment analysis, protein separations and electrophoresis, and how chemical probes are used for differential proteomic analysis. Graduate and advanced undergraduate students in proteomics should read and reread this section to internalize the logic of each technique; furthermore, seasoned researchers in related medical and bioanalytical fields may well gain a new understanding and respect for proteomic quantification capabilities. The chapters in this first section are high-quality mini-reviews with full bibliographies that will serve as excellent starting points for further reading.
In particular, Part I frames proteomics in terms of a large numbers problem that requires many approaches to be solved. If the human genome contains 30 000 genes, the human proteome is a far larger concept that must be described temporally and spatially in terms of multiple transcripts, with post-translational modifications as well as degradation and activation products (the editors, foreword, p. xi). Practical MS detection limits, described in Chapter 1 on the fundamentals of mass spectrometry (Veenstra, p. 4), are matched against the discussion of protein dynamic range within a cell (105 to 106) or in biological fluids such as serum (108 or 109) in Chapter 2 on 2D-PAGE (Gromov, Gromova and Celis, p. 21). It is entirely logical to consider chemical tagging for quantification (Brown & Fenselau) in Chapter 3 beside post-translational modifications in Chapter 4 (Conrads, Hood and Veenstra), both relying on careful mass analysis of peptide fragmentation patterns. The next Chapter (Tabb and Yates) contrasts these former ‘bottom-up’ approaches with ‘top-down’ proteomics methods using large-scale proteomic tandem mass spectrometry. After completing these analyses, the reader is correctly led to the realization that sample preparation is a necessary consideration for all proteomic analyses with protein fractionation methods described in Chapter 6 (Rabilloud). This suggests redefining protein chemistry tools, reverting somewhat from the reductionist view of purifying and analyzing a single protein entity in a controlled system, to a new global perspective of subfractionating proteomes into manageable sets of proteins, enriched for defined biochemical features.
Many proteomics reviews could be considered complete after Part I; however, this text devotes an additional two full sections to alternative methods which now build upon Part I and which present a number of opportunities for new bioinformatics tool development. Part II on ‘functional’ proteomics makes the important point that even though a set of co-purified proteins can coexist in a biochemically prepared sample, they do not necessarily interact within the cell. Functional association is defined here as directly interacting. Fluorescent proteins as tags for protein tracking can give temporal subcellular localization information; paired tags can also be used for FRET-based measurement of interactions in situ, described in Chapter 7 (Muller and Davis). A new MS ionization technique called nanoflow electrospray ionization described in Chapter 8 (Ilag and Robinson), is gentle enough to analyze large non-covalent protein complexes by increasing the m/z range of the mass spectrometer to be able to analyze high mass, multiply charged protein species. In Chapter 9, NMR is introduced as a high-throughput method for atomic level analysis of protein interactions (Clore). It is a computational feat that allows the terms ‘high-throughput’ and ‘NMR’ to be discussed in the same breath; Clore does an excellent job of describing how prior knowledge in the form of crystal structures for protein components can be assembled into models of protein complexes using limited intermolecular NOE data and residual dipolar coupling data. These three methods described in Part II are termed ‘functional’ proteomics approaches, because now proteins which coexist in a proteome can be connected by observable associations within the cellular milieu, and potentially at atomic resolution. Part II is not all-inclusive on protein–protein interactions techniques, but it is a thought-provoking discussion that emphasizes the need for new connections between proteins on proteomic lists for functional interpretation.
Part III describes alternative proteomics methods, which can be collected under the ‘new global protein quantification strategies’ heading, and which are at various stages of instrumental engineering. Chapter 10 on protein microarrays (Da Silva Baptista and Munroe) covers immunoaffinity-based array methods which can be practical and quantitative with careful calibration. Chapter 11 on microfluidics-based proteomics (Li et al.) describes several types of miniaturized sample preparation devices which can be connected with MS analyses. Single cell proteomics described in Chapter 12 (Dovichi et al.), reconnects with the earlier discussion in Part I of the proteomic numbers problem, with an excellent description of how the concept of average protein populations breaks down on the single cell scale. The ability to analyze proteins from single cells has direct applications in clinical proteomics where cellular heterogeneity and limited sample size are real considerations. An important discussion of ‘biomarkers’, proteins which can be correlated to a specific disease state, drug-response, or prognosis, is given in Chapter 13 (Prieto and Issaq). Biomarker discovery is a hot field at the moment; the challenges of this endeavor are multi-fold: potential biomarkers, at what may be vanishingly small levels in a sample, must be standardized for sample preparation, reproducibly detected, accurately quantified, and most critically, they must be validated as indicators of some clinical condition across hundreds of controlled patient samples. In Chapter 14 a discussion of how proteomics has been automated (Veenstra) is nicely paired with Chapter 15 on bioinformatics tools for proteomic analyses (Liebler). Indeed many of the chemical aspects of proteomic sample preparation, separation and MS analyses can be automated for standardized protocols, and important considerations for validation of protein ID's are given.
In summary, ‘Proteomics for Biological Discovery’ is a thorough compilation of discussions on the high demands placed upon biomedical proteomics for accurate identification and quantification of functionally linked protein species. We are very much still in the genomic era of collecting and identifying proteomes, in terms of subproteomes from cellular subfractions or organelles, tissue types and disease states. These component lists of proteins are critical to our understanding of biological systems. This text has very logically discussed three categories of proteomics methods. These include (i) the well-established methods, heavily dependent upon mass spectrometry and bioinformatics, as they are currently practiced; (ii) established instrumental techniques with new ‘omics interpretations, from microscopy to protein–protein interaction analysis and even to NMR; as well as (iii) brand-new methods which are still in the developmental stages of instrumental engineering for microscale and high-throughput analyses, enabled by microarray printing, microfluidic separations and single cell separations. This text is highly recommended as an update to any library which contains mass spectrometry, bioanalytical chemistry, medical, bioinformatics and genomic subjects.
Medicinal Chemistry & Molecular Pharmacology Department
Purdue University.
Bindley Bioscience Center at Purdue Discovery Park, 1203 West
State Street, West Lafayette, Indiana 47907-2057, USA
E-mail: gknudsen{at}pnhs.purdue.edu
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