Mass Spectrometry Data Analysis in Proteomics
Mass Spectrometry Data Analysis in Proteomics

Author: Rune Matthiesen

Publisher:

Published: 2013

Total Pages: 405

ISBN-13: 9781627033923

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Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably. Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics.

Neuroproteomics
Neuroproteomics

Author: Oscar Alzate

Publisher: CRC Press

Published: 2009-10-26

Total Pages: 356

ISBN-13: 1420076264

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In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we beg

Mass Spectrometry-Based Chemical Proteomics
Mass Spectrometry-Based Chemical Proteomics

Author: W. Andy Tao

Publisher: John Wiley & Sons

Published: 2019-07-10

Total Pages: 449

ISBN-13: 1118970217

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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.

Activity-Based Protein Profiling
Activity-Based Protein Profiling

Author: Benjamin F. Cravatt

Publisher: Springer

Published: 2019-01-25

Total Pages: 420

ISBN-13: 3030111431

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This volume provides a collection of contemporary perspectives on using activity-based protein profiling (ABPP) for biological discoveries in protein science, microbiology, and immunology. A common theme throughout is the special utility of ABPP to interrogate protein function and small-molecule interactions on a global scale in native biological systems. Each chapter showcases distinct advantages of ABPP applied to diverse protein classes and biological systems. As such, the book offers readers valuable insights into the basic principles of ABPP technology and how to apply this approach to biological questions ranging from the study of post-translational modifications to targeting bacterial effectors in host-pathogen interactions.

Quantitative Proteomics by Mass Spectrometry
Quantitative Proteomics by Mass Spectrometry

Author: Salvatore Sechi

Publisher: Methods in Molecular Biology

Published: 2018-04-15

Total Pages: 322

ISBN-13: 9781493980666

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This volume describes prominent methodologies developed by laboratories that have been leading the field of quantitative proteomics by mass spectrometry. The procedures for performing the experiments are described in an easy-to-understand manner with many technical details that usually are not reported in typical research articles. This second edition of Quantitative Proteomics by Mass Spectrometry provides a broad perspective of the methodologies used for quantifying proteins and post-translational modifications in different types of biomedical specimens. 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 thorough, Quantitative Proteomics by Mass Spectrometry, Second Edition is a valuable resource to help researchers understand and learn about the latest tools used in the study of quantitative proteomics by mass spectrometry.

Quantitative Methods in Proteomics
Quantitative Methods in Proteomics

Author: Katrin Marcus

Publisher: Humana Press

Published: 2012-06-08

Total Pages: 539

ISBN-13: 9781617798849

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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.

Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics
Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics

Author: Mahmud Hossain

Publisher: Springer Nature

Published: 2020-09-26

Total Pages: 283

ISBN-13: 3030534332

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Covering a wide-ranging facet of a “gold-standard” targeted mass spectrometry (MS) method for the consistent detection and accurate quantification of preselected proteins in complex biological matrices, Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics: A Comprehensive View describes: The knowledge-based development of highly efficient SRM methodology including assay workflow, selection of proteins, peptides, transitions and its validation, and quality assessment Available bioinformatic tools – for both pre-acquisition method development and post-MS acquisition data analysis and data repositories Various relative and absolute quantification techniques SRM-MS’ widespread applications in biomarker development and in clinical studies, as well as in the analysis of various posttranslational modifications (PTMs) Current challenges and contemporary trends to overcome those difficulties In addition, it features the historical development of modern-day mass spectrometry with its vivid applications and also covers basic MS instrumentation, ionization techniques, and various proteomics approaches. Comprehensive discussion, extensive references at the end of each chapter, and the list of review articles in the bibliography offer invaluable resources for advanced readings. Researchers from the undergraduate to postgraduate level and beyond in both academic or industry settings studying and working on mass spectrometry and/or proteomics will benefit from this book.

Proteomic and Metabolomic Approaches to Biomarker Discovery
Proteomic and Metabolomic Approaches to Biomarker Discovery

Author: Haleem J. Issaq

Publisher: Academic Press

Published: 2013-05-20

Total Pages: 489

ISBN-13: 0123947952

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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 Informatics
Proteome Informatics

Author: Conrad Bessant

Publisher: Royal Society of Chemistry

Published: 2016-11-15

Total Pages: 429

ISBN-13: 1782626735

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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.

Proteomics Sample Preparation
Proteomics Sample Preparation

Author: Jörg von Hagen

Publisher: John Wiley & Sons

Published: 2011-08-24

Total Pages: 498

ISBN-13: 3527644695

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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.