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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.

Book Synopsis Mass Spectrometry Data Analysis in Proteomics by : Rune Matthiesen

Download or read book Mass Spectrometry Data Analysis in Proteomics written by Rune Matthiesen and published by . This book was released on 2013 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Mass Spectrometry Data Analysis in Proteomics

Author: Rune Matthiesen

Publisher: Springer Science & Business Media

Published: 2008-02-02

Total Pages: 322

ISBN-13: 1597452750

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This is an in-depth guide to the theory and practice of analyzing raw mass spectrometry (MS) data in proteomics. The volume outlines available bioinformatics programs, algorithms, and databases available for MS data analysis. General guidelines for data analysis using search engines such as Mascot, Xtandem, and VEMS are provided, with specific attention to identifying poor quality data and optimizing search parameters.

Book Synopsis Mass Spectrometry Data Analysis in Proteomics by : Rune Matthiesen

Download or read book Mass Spectrometry Data Analysis in Proteomics written by Rune Matthiesen and published by Springer Science & Business Media. This book was released on 2008-02-02 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is an in-depth guide to the theory and practice of analyzing raw mass spectrometry (MS) data in proteomics. The volume outlines available bioinformatics programs, algorithms, and databases available for MS data analysis. General guidelines for data analysis using search engines such as Mascot, Xtandem, and VEMS are provided, with specific attention to identifying poor quality data and optimizing search parameters.

Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry

Author: Susmita Datta

Publisher: Springer

Published: 2016-12-15

Total Pages: 295

ISBN-13: 3319458094

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This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass spectrometry, time-of-flight data, and Fourier transform mass spectrometry are but a selection of the measurement platforms available to the modern analyst. Thus in practical proteomics or metabolomics, researchers will not only be confronted with new high dimensional data types—as opposed to the familiar data structures in more classical genomics—but also with great variation between distinct types of mass spectral measurements derived from different platforms, which may complicate analyses, comparison, and interpretation of results.

Book Synopsis Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry by : Susmita Datta

Download or read book Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry written by Susmita Datta and published by Springer. This book was released on 2016-12-15 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass spectrometry, time-of-flight data, and Fourier transform mass spectrometry are but a selection of the measurement platforms available to the modern analyst. Thus in practical proteomics or metabolomics, researchers will not only be confronted with new high dimensional data types—as opposed to the familiar data structures in more classical genomics—but also with great variation between distinct types of mass spectral measurements derived from different platforms, which may complicate analyses, comparison, and interpretation of results.

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

Book Synopsis Neuroproteomics by : Oscar Alzate

Download or read book Neuroproteomics written by Oscar Alzate and published by CRC Press. This book was released on 2009-10-26 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Proteomics Data Analysis

Author: Daniela Cecconi

Publisher:

Published: 2021

Total Pages: 326

ISBN-13: 9781071616413

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This thorough book collects methods and strategies to analyze proteomics data. It is intended to describe how data obtained by gel-based or gel-free proteomics approaches can be inspected, organized, and interpreted to extrapolate biological information. Organized into four sections, the volume explores strategies to analyze proteomics data obtained by gel-based approaches, different data analysis approaches for gel-free proteomics experiments, bioinformatic tools for the interpretation of proteomics data to obtain biological significant information, as well as methods to integrate proteomics data with other omics datasets including genomics, transcriptomics, metabolomics, and other types of data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that will ensure high quality results in the lab. Authoritative and practical, Proteomics Data Analysis serves as an ideal guide to introduce researchers, both experienced and novice, to new tools and approaches for data analysis to encourage the further study of proteomics.

Book Synopsis Proteomics Data Analysis by : Daniela Cecconi

Download or read book Proteomics Data Analysis written by Daniela Cecconi and published by . This book was released on 2021 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough book collects methods and strategies to analyze proteomics data. It is intended to describe how data obtained by gel-based or gel-free proteomics approaches can be inspected, organized, and interpreted to extrapolate biological information. Organized into four sections, the volume explores strategies to analyze proteomics data obtained by gel-based approaches, different data analysis approaches for gel-free proteomics experiments, bioinformatic tools for the interpretation of proteomics data to obtain biological significant information, as well as methods to integrate proteomics data with other omics datasets including genomics, transcriptomics, metabolomics, and other types of data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that will ensure high quality results in the lab. Authoritative and practical, Proteomics Data Analysis serves as an ideal guide to introduce researchers, both experienced and novice, to new tools and approaches for data analysis to encourage the further study of proteomics.

Introducing Proteomics

Author: Josip Lovric

Publisher: John Wiley & Sons

Published: 2011-06-17

Total Pages: 310

ISBN-13: 1119957192

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Introducing Proteomics gives a concise and coherent overview of every aspect of current proteomics technology, which is a rapidly developing field that is having a major impact within the life and medical sciences. This student-friendly book, based on a successful course developed by the author, provides its readers with sufficient theoretical background to be able to plan, prepare, and analyze a proteomics study. The text covers the following: Separation Technologies Analysis of Peptides/Proteins by Mass Spectrometry Strategies in Proteomics This contemporary text also includes numerous examples and explanations for why particular strategies are better than others for certain applications. In addition, Introducing Proteomics includes extensive references and a list of relevant proteomics information sources; essential for any student. This no-nonsense approach to the subject tells students exactly what they need to know, leaving out unnecessary information. The student companion site enhances learning and provides answers to the end of chapter problems. "I think this book will be a popular and valuable resource for students and newcomers to the field who would like to have an overview and initial understanding of what proteomics is about. The contents are well organized and address the major issues." —Professor Walter Kolch, Director, Systems Biology Ireland & Conway Institute, University College Dublin Companion Website www.wiley.com/go/lovric

Book Synopsis Introducing Proteomics by : Josip Lovric

Download or read book Introducing Proteomics written by Josip Lovric and published by John Wiley & Sons. This book was released on 2011-06-17 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introducing Proteomics gives a concise and coherent overview of every aspect of current proteomics technology, which is a rapidly developing field that is having a major impact within the life and medical sciences. This student-friendly book, based on a successful course developed by the author, provides its readers with sufficient theoretical background to be able to plan, prepare, and analyze a proteomics study. The text covers the following: Separation Technologies Analysis of Peptides/Proteins by Mass Spectrometry Strategies in Proteomics This contemporary text also includes numerous examples and explanations for why particular strategies are better than others for certain applications. In addition, Introducing Proteomics includes extensive references and a list of relevant proteomics information sources; essential for any student. This no-nonsense approach to the subject tells students exactly what they need to know, leaving out unnecessary information. The student companion site enhances learning and provides answers to the end of chapter problems. "I think this book will be a popular and valuable resource for students and newcomers to the field who would like to have an overview and initial understanding of what proteomics is about. The contents are well organized and address the major issues." —Professor Walter Kolch, Director, Systems Biology Ireland & Conway Institute, University College Dublin Companion Website www.wiley.com/go/lovric

Mass Spectrometry-Based Chemical Proteomics

Author: W. Andy Tao

Publisher: John Wiley & Sons

Published: 2019-07-10

Total Pages: 448

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.

Book Synopsis Mass Spectrometry-Based Chemical Proteomics by : W. Andy Tao

Download or read book Mass Spectrometry-Based Chemical Proteomics written by W. Andy Tao and published by John Wiley & Sons. This book was released on 2019-07-10 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Quantitative Proteomics by Mass Spectrometry

Author: Salvatore Sechi

Publisher: Humana

Published: 2016-02-12

Total Pages: 0

ISBN-13: 9781493935222

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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.

Book Synopsis Quantitative Proteomics by Mass Spectrometry by : Salvatore Sechi

Download or read book Quantitative Proteomics by Mass Spectrometry written by Salvatore Sechi and published by Humana. This book was released on 2016-02-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Processing Metabolomics and Proteomics Data with Open Software

Author: Robert Winkler

Publisher: Royal Society of Chemistry

Published: 2020-03-19

Total Pages: 460

ISBN-13: 1788017218

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Metabolomics and proteomics allow deep insights into the chemistry and physiology of biological systems. This book expounds open-source programs, platforms and programming tools for analysing metabolomics and proteomics mass spectrometry data. In contrast to commercial software, open-source software is created by the academic community, which facilitates the direct interaction between users and developers and accelerates the implementation of new concepts and ideas. The first section of the book covers the basics of mass spectrometry, experimental strategies, data operations, the open-source philosophy, metabolomics, proteomics and statistics/ data mining. In the second section, active programmers and users describe available software packages. Included tutorials, datasets and code examples can be used for training and for building custom workflows. Finally, every reader is invited to participate in the open science movement.

Book Synopsis Processing Metabolomics and Proteomics Data with Open Software by : Robert Winkler

Download or read book Processing Metabolomics and Proteomics Data with Open Software written by Robert Winkler and published by Royal Society of Chemistry. This book was released on 2020-03-19 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics and proteomics allow deep insights into the chemistry and physiology of biological systems. This book expounds open-source programs, platforms and programming tools for analysing metabolomics and proteomics mass spectrometry data. In contrast to commercial software, open-source software is created by the academic community, which facilitates the direct interaction between users and developers and accelerates the implementation of new concepts and ideas. The first section of the book covers the basics of mass spectrometry, experimental strategies, data operations, the open-source philosophy, metabolomics, proteomics and statistics/ data mining. In the second section, active programmers and users describe available software packages. Included tutorials, datasets and code examples can be used for training and for building custom workflows. Finally, every reader is invited to participate in the open science movement.

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.

Book Synopsis Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics by : Mahmud Hossain

Download or read book Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics written by Mahmud Hossain and published by Springer Nature. This book was released on 2020-09-26 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.