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Hands-on researchers describe in step-by-step detail 73 proven laboratory methods and bioinformatics tools essential for analysis of the proteome. These cutting-edge techniques address such important tasks as sample preparation, 2D-PAGE, gel staining, mass spectrometry, and post-translational modification. There are also readily reproducible methods for protein expression profiling, identifying protein-protein interactions, and protein chip technology, as well as a range of newly developed methodologies for determining the structure and function of a protein. The bioinformatics tools include those for analyzing 2D-GEL patterns, protein modeling, and protein identification. All laboratory-based protocols follow the successful Methods in Molecular BiologyTM series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
A compendium of thirty-four powerful techniques for identifying and analyzing the diversity of proteins expressed in cells. Thee readily reproducible proteomic methods range from general to specific techniques, and include methods for data analysis, posttranslational modification, and its variants and isoforms. Additional methods demonstrate the application of proteomics to the discovery of serological tumor markers, to identifying the determinants of sensitivity to antitumor drugs, and to specialized fields, such as endocrinology, plant biology, nephrology, and urology.
The authors are commonly the techniques" originators, and each has demonstrated a hands-on mastery of the methods described, always fine-tuning them here for optimal productivity.
Driven by the widespread growth of proteomic practices, protein separation techniques have been refined to minimize variability, optimize particular applications, and adapt to user preferences in the analysis of proteins. Separation Methods in Proteomics provides a comprehensive examination of all major separation techniques for proteomic
This book focuses on the advantages and disadvantages of each of the commonly used quantitative proteomic methods in terms of accuracy, sensitivity, and reproducibility. It also concentrates on the effective applications of these methods that resulted in many discoveries of the role of the proteins expressed in living cells and biological fluids. The first part of the book focuses on the description of advantages and disadvantages of each of the commonly used quantitative proteomic methods in terms of accuracy, sensitivity, and, especially, reproducibility. The second part of the book focuses on providing concise descriptions of the effective applications of these methods to demonstrate how they have resulted in many important discoveries of the roles of the proteins expressed in living cells.
This second edition expands upon the previous edition with current, detailed developments in the field and brings together a multi-disciplinary team of leading researchers to provide their latest protocols for clinical proteomics analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and Practical, Clinical Proteomics: Methods and Protocols, Second Edition presents approaches that will serve as a reliable guide to researchers, including clinicians, chemists, molecular biologists, bioinformaticians and computational, biologists, and investigators working on biomarker development.
Principles of Proteomics is designed specifically to explain the different stages of proteomic analysis, their complexities and their jargon to students and researchers in a non-technical overview of the field. The author describes the broad range of problems which proteomics can address, including structural proteomics, interaction proteomics, protein modification analysis and functional proteomics. Methodologies are described in user-friendly language, from the more traditional two-dimensional gel electrophoresis to the new developments in protein chip technologies. These are well presented in the context of overall strategies which can be adopted to address the different aspects of large-scale protein analysis.
Still the only concise practical guide to laboratory experiments in proteomics, this new edition now also covers DIGE technology and liquid-chromatography, while the troubleshooting section has been considerably extended. Adopting a practical approach, the authors present the relevant techniques and explain the route to successful experimental design and optimal method selection. They cover such electrophoretic techniques as isoelectric focusing, SDS page, 2-D page, and DIGE, as well as liquid-chromatography techniques, such as ion exchange, affinity chromatography and reversed-phase HPLC. Mass-spectrometric techniques include MALDI, ESI, and FT ICR. Generously illustrated, partly in color, the book also features updates of protocols as well as animations illustrating crucial methodological steps on a companion website.
Protein modifications and changes made to them, as well as the quantities of expressed proteins, can define the various functional stages of the cell. Accordingly, perturbations can lead to various diseases and disorders. As a result, it has become paramount to be able to detect and monitor post-translational modifications and to measure the abundance of proteins within the cell with extreme sensitivity. While protein identification is an almost routine requirement nowadays, reliable techniques for quantifying unmodified proteins (including those that escape detection under standard conditions, such as protein isoforms and membrane proteins) is not routine. Quantitative Methods in Proteomics gives a detailed survey of topics and methods on the principles underlying modern protein analysis, from statistical issues when planning proteomics experiments, to gel-based and mass spectrometry-based applications. The quantification of post-translational modifications is also addressed, followed by the “hot” topics of software and data analysis, as well as various overview chapters which provide a comprehensive overview of existing methods in quantitative proteomics. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Quantitative Methods in Proteomics serves as a comprehensive and competent overview of the important and still growing field of quantitative proteomics.
With the completion of sequencing projects and the advancement of a- lytical tools for protein identification, proteomics—the study of the expressed part of the genome—has become a major region of the burgeoning field of functional genomics. High-resolution 2-D gels can reveal virtually all p- teins present in a cell or tissue at any given time, including posttranslationally modified proteins. Changes in the expression and structure of most cellular proteins caused by differentiation or external stimuli can be displayed and eventually identified using 2-D protein gels. 2-D Proteome Analysis Protocols covers all aspects of the use of 2-D protein electrophoresis for the analysis of biological problems. The contri- tors include many of the leaders in the fields of biochemistry and analytical chemistry who were instrumental in the development of high-resolution 2-D gels, immobilized pH gradients, computer analysis, and mass spectromet- based protein identification methodologies. This book is intended as a benchtop manual and guide both for novices to 2-D gels and for those aficionados who wish to try the newer techniques. Any group using protein biochemistry—especially in the fields of molecular biology, biochemistry, microbiology, and cell biology—should find this book eminently useful. 2-D Proteome Analysis Protocols takes the researcher through the c- plete process of working with 2-D protein gels from making the protein - tract to finally identifying the proteins of interest. It includes protocols for generating 2-D protein extracts from most of the standard model organisms, including bacteria, yeast, nematode, Drosophila, plants, mouse, and human.