Proteomic Profiling and Analytical Chemistry


Book Description

Proteomic Profiling and Analytical Chemistry: The Crossroads, Second Edition helps scientists without a strong background in analytical chemistry to understand principles of the multistep proteomic experiment necessary for its successful completion. It also helps researchers who do have an analytical chemistry background to break into the proteomics field. Highlighting points of junction between proteomics and analytical chemistry, this resource links experimental design with analytical measurements, data analysis, and quality control. This targeted point of view will help both biologists and chemists to better understand all components of a complex proteomic study. The book provides detailed coverage of experimental aspects such as sample preparation, protein extraction and precipitation, gel electrophoresis, microarrays, dynamics of fluorescent dyes, and more. The key feature of this book is a direct link between multistep proteomic strategy and quality control routinely applied in analytical chemistry. This second edition features a new chapter on SWATH-MS, substantial updates to all chapters, including proteomic database search and analytical quantification, expanded discussion of post-hoc statistical tests, and additional content on validation in proteomics. - Covers the analytical consequences of protein and peptide modifications that may have a profound effect on how and what researchers actually measure - Includes practical examples illustrating the importance of problems in quantitation and validation of biomarkers - Helps in designing and executing proteomic experiments with sound analytics




Proteomic Profiling


Book Description

This detailed new edition presents the latest developments of the main pillars of protein analysis, namely sample preparation, separation, and characterization. Core areas in this volume are protocols for the analysis of post-translational modifications and protein interaction partners, followed by sophisticated procedures to enrich for extracellular vesicles and organelles, along with several types of protein immuno-assays complemented by various methods for the characterization of antibodies and host-cell protein analysis. Last but not least, a few standard sample preparation protocols and recent advances concerning immuno-chemical detection of proteins are included as well. Written for the highly successful Methods in Molecular Biology series, 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 up-to-date, Proteomic Profiling: Methods and Protocols, Second Edition serves as an ideal reference for students of biochemistry, biomedicine, biology, and genomics and will be an invaluable source for the experienced, practicing scientist as well.




Proteomic and Metabolomic Approaches to Biomarker Discovery


Book Description

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




Proteome Analysis


Book Description

This book explores the current status of proteomics, an exciting new discipline, which is less than 10 years old. This new field has rapidly grown into a major commercial and research enterprise with great prospects for dramatically advancing our knowledge of basic biological and disease processes. The contributors to this book are an international panel of proteomics experts, who review and discuss the current status of specific technologies and approaches. Proteomics represents an exciting new way to pursue biological and biomedical science at an unprecedented pace. Proteomics takes a broad, comprehensive, systematic approach to understanding biology that is generally unbiased and not dependent upon existing knowledge. The major components of proteomics from basic discovery using a range of alternative analytical methods to discovery validation and use for clinical applications are discussed. State-of-the-art protein profiling methods include high resolution two-dimensional gels, two-dimensional differential in-gel electrophoresis, LC-MS and LC-MS/MS using accurate mass tags, and protein identifications of proteins from gels using mass spectrometry methods are discussed in depth. Other chapters describe comprehensive characterization of proteomes using electrophoretic prefractionation and analyses of sub-proteomes based on specific posttranslational modifications including the phospho-proteome, the glyco-proteome, and nitrated proteins. These conventional proteome analysis chapters are complemented by discussion of emerging technologies and approaches such as affinity based biosensor proteomics as well as the use of protein microarrays, microfluidics and nanotechnology. Strategies for improving throughput by automation are also discussed. Additional chapters address the application of current proteome techniques to clinical problems and the availability of protein expression library resources for proteome studies.· Authored by international experts in the field · Covers a wide range of topics including 2-D gels, global proteomics using accurate mass tags, global proteomics using electrophoretic prefractionation, microfluidics, and nanotechnology· Includes state-of-the-art protein profiling methods, and emerging technologies




Applications in Forensic Proteomics


Book Description

Introduction to forensic proteomics -- A proteomics tutorial -- Proteomic sample preparation techniques : toward forensic proteomic applications -- NextGen serology : leveraging mass spectrometry for protein-based human body fluid identification -- Informatics approaches to forensic body fluid identification by proteomic mass spectrometry -- Fingermarks as a new proteomic specimen : state of the art and perspective of in situ proteomics -- Human identification using genetically variant peptides in biological forensic evidence -- Proteomics in the analysis of forensic, archaeological, and paleontological bone -- Proteomics for microbial forensics -- ISO 17025 accreditation of method-based mass spectrometry for bioforensic analyses -- Unambiguous identification of ricin and abrin with advanced mass spectrometric assays -- Challenges in the development of reference materials for protein toxins -- The statistical defensibility of forensic proteomics.




Mass Spectrometry-Based Chemical Proteomics


Book Description

PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.




Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis


Book Description

It is evident that biochemical control is not strictly hierarchical and that intermediary metabolism can contribute to control of regulatory pathways. Metabolic studies are therefore increasingly important in gene function analyses, and an increased interest in metabolites as biomarkers for disease progression or response to therapeutic intervention is also evident in the pharmaceutical industry. This book offers guidelines to currently available technology and bioinformatics and database strategies now being developed. Evidence is presented that metabolic profiling is a valuable addition to genomics and proteomics strategies devoted to drug discovery and development, and that metabolic profiling offers numerous advantages.




Proteomics for Biological Discovery


Book Description

Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.




Target Discovery and Validation


Book Description

The modern drug developers? guide for making informed choices among the diverse target identification methods Target Discovery and Validation: Methods and Strategies for Drug Discovery offers a hands-on review of the modern technologies for drug target identification and validation. With contributions from noted industry and academic experts, the book addresses the most recent chemical, biological, and computational methods. Additionally, the book highlights techologies that are applicable to ?difficult? targets and drugs directed at multiple targets, including chemoproteomics, activity-based protein profiling, pathway mapping, genome-wide association studies, and array-based profiling. Throughout, the authors highlight a range of diverse approaches, and target validation studies reveal how these methods can support academic and drug discovery scientists in their target discovery and validation research. This resource: -Offers a guide to identifying and validating targets, a key enabling technology without which no new drug development is possible -Presents the information needed for choosing the appropriate assay method from the ever-growing range of available options -Provides practical examples from recent drug development projects, e. g. in kinase inhibitor profiling Written for medicinal chemists, pharmaceutical professionals, biochemists, biotechnology professionals, and pharmaceutical chemists, Target Discovery and Validation explores the current methods for the identification and validation of drug targets in one comrpehensive volume. It also includes numerous practical examples.




Genomics, Proteomics, and Metabolomics


Book Description

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.