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This book presents a compilation of methods that detail improved protein and peptide sample preparation and identification. Chapters guide readers through methods for depletion of myofibril-associated proteins, peptide sample preparation in urinary proteomics, purification of targeted proteins from native tissues, fractionation strategies for protein analysis, and GeLC-MS as a sample preparation method for sample preparation for proteomics using minimal amount of tissue. 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, Tissue Proteomics: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.
Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research. - Describes the use of biomarkers to reduce clinical errors in research - Includes techniques from a range of biomarker discoveries - Covers all steps involved in biomarker discovery, from study design to study execution
In one volume this book provides useful and innovative protocols developed specifically for the proteomic profiling of human tissues. The book provides high-throughput gel-based techniques, microarrays and a number of other methods used in proteomic research. This important book will prove indispensable to investigators of biomarker discovery and therapeutic response profiling, as well as those forging new paths in the fields of theranostics and personalized medicine.
This long-awaited first guide to sample preparation for proteomics studies overcomes a major bottleneck in this fast growing technique within the molecular life sciences. By addressing the topic from three different angles -- sample, method and aim of the study -- this practical reference has something for every proteomics researcher. Following an introduction to the field, the book looks at sample preparation for specific techniques and applications and finishes with a section on the preparation of sample types. For each method described, a summary of the pros and cons is given, as well as step-by-step protocols adaptable to any specific proteome analysis task.
The definitive guide to peptidomics- a hands-on lab reference The first truly comprehensive book about peptidomics for protein and peptide analysis, this reference provides a detailed description of the hows and whys of peptidomics and how the techniques have evolved. With chapters contributed by leading experts, it covers naturally occurring peptides, peptidomics methods and new developments, and the peptidomics approach to biomarker discovery. Explaining both the principles and the applications, Peptidomics: Methods and Applications: * Features examples of applications in diverse fields, including pharmaceutical science, toxicity biomarkers, and neuroscience * Details the successful peptidomic analyses of biological material ranging from plants to mammals * Describes a cross section of analytical techniques, including traditional methodologies, emerging trends, and new techniques for high throughput approaches An enlightening reference for experienced professionals, this book is sufficiently detailed to serve as a step-by-step guide for beginning researchers and an excellent resource for students taking biotechnology and proteomics courses. It is an invaluable reference for protein chemists and biochemists, professionals and researchers in drug and biopharmaceutical development, analytical and bioanalytical chemists, toxicologists, and others.
The field of proteomics has developed rapidly over the past decade nurturing the need for a detailed introduction to the various informatics topics that underpin the main liquid chromatography tandem mass spectrometry (LC-MS/MS) protocols used for protein identification and quantitation. Proteins are a key component of any biological system, and monitoring proteins using LC-MS/MS proteomics is becoming commonplace in a wide range of biological research areas. However, many researchers treat proteomics software tools as a black box, drawing conclusions from the output of such tools without considering the nuances and limitations of the algorithms on which such software is based. This book seeks to address this situation by bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, so that users of proteomics data can be confident that they are using appropriate tools in suitable ways.
This book provides thorough coverage of high-throughput OMICs technologies for the monitoring of stem cells and regenerative medicine. Specific topics covered include the genomics, proteomics, and metabolomics aspects of regenerative medicine, metabolic profiling of mesenchymal stem cells, genome profiling of mesenchymal stem cells, OMICs monitoring of stem cell-derived exosomes, stem cell proteomics, lipidomics, OMICs profiling of cancer (stem) cells, and finally ethical considerations of OMICs-based investigations. Chapters are authored by world-renowned scientists who have valuable expertise in the field of OMICs and regenerative medicine. Genomics, Proteomics, and Metabolomics: Stem Cells Monitoring in Regenerative Medicine, part of Springer’s Stem Cell Biology and Regenerative Medicine series, is essential reading for researchers, clinicians, biologists, biochemists, and pharmaceutical experts conducting research in the fields of stem cell biology, molecular aspects of stem cell research, tissue engineering, regenerative medicine, cellular therapy, OMICs, bioinformatics, and ethics.
Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.
Proteomics and peptidomics is the detailed understanding of the role that proteins and peptides play in health and disease and is a necessary compliment to genetic analysis. The functional expression analysis of both proteins and peptides plays a central role in modern drug discovery as well as drug development, and is also a key research area in systems biology. Proteomics and Peptidomics captures the width as well as the depth within the area and exemplifies the variety as well as the traditional basis of analytical chemistry that is needed in order to move forward in expression analysis studies. As a fast emerging field, it gives and overview of parts within the field combined with highly specialized and dedicated topics that are intended to compliment each other.
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.