Quantitative Proteomics By Mass Spectrometry

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Quantitative Proteomics by Mass Spectrometry

Salvatore Sechi
Quantitative Proteomics by Mass Spectrometry Book PDF

Author : Salvatore Sechi
Publisher : Methods in Molecular Biology
Page : 322 pages
File Size : 52,9 Mb
Release : 2018-04-15
Category : Science
ISBN : 1493980661

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Quantitative Proteomics by Mass Spectrometry by Salvatore Sechi Pdf

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 Proteomics by Mass Spectrometry

Salvatore Sechi
Quantitative Proteomics by Mass Spectrometry Book PDF

Author : Salvatore Sechi
Publisher : Springer Science & Business Media
Page : 223 pages
File Size : 40,8 Mb
Release : 2008-02-05
Category : Science
ISBN : 9781597452557

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Quantitative Proteomics by Mass Spectrometry by Salvatore Sechi Pdf

This volume is a compendium of cutting-edge protocols for quantitative proteomics, and presents the most significant methods used in the field today. The focus on mass spectrometry (MS) is integral. Attention is given to state-of-the-art techniques for the characterization of the phosphoproteome and tandem MS for detection of inborn errors of metabolism. This volume is an indispensable resource in the search for novel biomarkers.

Quantitative Methods in Proteomics

Katrin Marcus
Quantitative Methods in Proteomics Book PDF

Author : Katrin Marcus
Publisher : Humana Press
Page : 539 pages
File Size : 52,8 Mb
Release : 2012-06-08
Category : Science
ISBN : 1617798843

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Quantitative Methods in Proteomics by Katrin Marcus Pdf

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.

Quantitative Proteomics

Claire E Eyers,Simon Gaskell
Quantitative Proteomics Book PDF

Author : Claire E Eyers,Simon Gaskell
Publisher : Royal Society of Chemistry
Page : 128 pages
File Size : 40,8 Mb
Release : 2014-01-10
Category : Science
ISBN : 9781782621096

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Quantitative Proteomics by Claire E Eyers,Simon Gaskell Pdf

As a component of post-genome science, the field of proteomics has assumed great prominence in recent years. Whereas quantitative analyses focussed initially on relative quantification, a greater emphasis is now placed on absolute quantification and consideration of proteome dynamics. Coverage of the topic of quantitative proteomics requires consideration both of the analytical fundamentals of quantitative mass spectrometry and the specific demands of the problem being addressed. Quantitative Proteomics aims to outline the state of the art in mass spectrometry-based quantitative proteomics, describing recent advances and current limitations in the instrumentation used, together with the various methods employed for generating high quality data. Details on both strategies describing how stable isotope labelling can be applied and methods for performing quantitative analysis of proteins in a label-free manner are given. The utility of these strategies to understanding cellular protein dynamics are then exemplified with chapters looking at spatial proteomics, dynamics of protein function as determined by quantifying changes in protein post-translational modification and protein turnover. Finally, a key application of these techniques to biomarker discovery and validation is presented, together with the rapidly developing area of quantitative analysis of protein-based foodstuffs. This exemplary book is essential reading for analytical and biological mass spectrometrists working in proteomics research, as well as those undertaking either fundamental or clinical-based investigations with an interest in understanding protein dynamics and/or biomarker assessment.

Quantitative Methods in Proteomics

Katrin Marcus,Martin Eisenacher,Barbara Sitek
Quantitative Methods in Proteomics Book PDF

Author : Katrin Marcus,Martin Eisenacher,Barbara Sitek
Publisher : Unknown
Page : 483 pages
File Size : 47,7 Mb
Release : 2021
Category : Proteomics
ISBN : 1071610244

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Quantitative Methods in Proteomics by Katrin Marcus,Martin Eisenacher,Barbara Sitek Pdf

This second edition provides new and updated methods on the principles underlying modern protein analysis, from statistical issues to gel-based and mass spectrometry-based applications. Chapters detail protein quantification as basis for realisation of quantitative studies, gel-based and mass spectrometry-based quantification techniques, TMT, IPTL, PRM, MALDI Imaging, SILAC, PTM analysis, DIA, cross-linking, and the up-to-date topics of software and data 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 cutting-edge, Quantitative Methods in Proteomics, Second Edition aims to provide comprehensive and competent overview in the important and still growing field of quantitative proteomics.

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry

Ingvar Eidhammer,Harald Barsnes,Geir Egil Eide,Lennart Martens
Computational and Statistical Methods for Protein Quantification by Mass Spectrometry Book PDF

Author : Ingvar Eidhammer,Harald Barsnes,Geir Egil Eide,Lennart Martens
Publisher : John Wiley & Sons
Page : 290 pages
File Size : 40,5 Mb
Release : 2012-12-10
Category : Mathematics
ISBN : 9781118493779

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Computational and Statistical Methods for Protein Quantification by Mass Spectrometry by Ingvar Eidhammer,Harald Barsnes,Geir Egil Eide,Lennart Martens Pdf

The definitive introduction to data analysis in quantitative proteomics This book provides all the necessary knowledge about mass spectrometry based proteomics methods and computational and statistical approaches to pursue the planning, design and analysis of quantitative proteomics experiments. The author’s carefully constructed approach allows readers to easily make the transition into the field of quantitative proteomics. Through detailed descriptions of wet-lab methods, computational approaches and statistical tools, this book covers the full scope of a quantitative experiment, allowing readers to acquire new knowledge as well as acting as a useful reference work for more advanced readers. Computational and Statistical Methods for Protein Quantification by Mass Spectrometry: Introduces the use of mass spectrometry in protein quantification and how the bioinformatics challenges in this field can be solved using statistical methods and various software programs. Is illustrated by a large number of figures and examples as well as numerous exercises. Provides both clear and rigorous descriptions of methods and approaches. Is thoroughly indexed and cross-referenced, combining the strengths of a text book with the utility of a reference work. Features detailed discussions of both wet-lab approaches and statistical and computational methods. With clear and thorough descriptions of the various methods and approaches, this book is accessible to biologists, informaticians, and statisticians alike and is aimed at readers across the academic spectrum, from advanced undergraduate students to post doctorates entering the field.

Mass Spectrometry-Based Chemical Proteomics

W. Andy Tao,Ying Zhang
Mass Spectrometry Based Chemical Proteomics Book PDF

Author : W. Andy Tao,Ying Zhang
Publisher : John Wiley & Sons
Page : 448 pages
File Size : 52,5 Mb
Release : 2019-07-31
Category : Science
ISBN : 9781118970201

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Mass Spectrometry-Based Chemical Proteomics by W. Andy Tao,Ying Zhang Pdf

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.

Application of Selected Reaction Monitoring to Highly Multiplexed Targeted Quantitative Proteomics

Michael Kinter,Caroline S. Kinter
Application of Selected Reaction Monitoring to Highly Multiplexed Targeted Quantitative Proteomics Book PDF

Author : Michael Kinter,Caroline S. Kinter
Publisher : Springer Science & Business Media
Page : 65 pages
File Size : 40,5 Mb
Release : 2013-09-17
Category : Medical
ISBN : 9781461486664

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Application of Selected Reaction Monitoring to Highly Multiplexed Targeted Quantitative Proteomics by Michael Kinter,Caroline S. Kinter Pdf

A key experiment in biomedical research is monitoring the expression of different proteins in order to detect changes that occur in biological systems under different experimental conditions. The method that is most widely used is the Western blot analysis. While Western blot is a workhorse in laboratories studying protein expression and has several advantages, it also has a number of significant limitations. In particular, the method is semi-quantitative with limited dynamic range. Western blot focuses on a single protein per sample with only a small number of representative samples analyzed in an experiment. New quantitative tools have been needed for some time to at least supplement, & possibly replace, the Western blot. Mass spectrometric methods have begun to compete with Western blot for routine quantitative analyses of proteins. One of these methods is based on the tandem mass spectrometry technique of selected reaction monitoring (SRM), which is also called multiple reaction monitoring (MRM). Selected reaction monitoring is actually an older tandem mass spectrometry technique, first described in the late 70s, that is widely utilized in the quantitative analysis of small molecules like drugs & metabolites. The use of selected reaction monitoring for the quantitative analysis of proteins has a number of advantages. Most importantly, it is fundamentally quantitative with a wide dynamic range. The output of the analysis is a numerical result that can range over several orders of magnitude. Other advantages include sufficient specificity & sensitivity to detect low abundance proteins in complex mixtures. Finally, selected reaction monitoring can be multiplexed to allow the quantitative analysis of relatively large numbers of proteins in a single sample in a single experiment. This Brief will explain both the theoretical & experimental details of the selected reaction monitoring experiment as it is applied to proteins. ​

Quantitative Proteome Analysis

Kazuhiro Imai,Sam Li Fong Yau
Quantitative Proteome Analysis Book PDF

Author : Kazuhiro Imai,Sam Li Fong Yau
Publisher : CRC Press
Page : 314 pages
File Size : 47,6 Mb
Release : 2013-08-05
Category : Science
ISBN : 9789814316514

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Quantitative Proteome Analysis by Kazuhiro Imai,Sam Li Fong Yau Pdf

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.

Mass Spectrometry Data Analysis in Proteomics

Rune Matthiesen
Mass Spectrometry Data Analysis in Proteomics Book PDF

Author : Rune Matthiesen
Publisher : Unknown
Page : 405 pages
File Size : 40,5 Mb
Release : 2013
Category : Mass spectrometry
ISBN : 1627033920

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Mass Spectrometry Data Analysis in Proteomics by Rune Matthiesen Pdf

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

Rune Matthiesen
Mass Spectrometry Data Analysis in Proteomics Book PDF

Author : Rune Matthiesen
Publisher : Springer Science & Business Media
Page : 322 pages
File Size : 49,7 Mb
Release : 2008-02-02
Category : Science
ISBN : 9781597452755

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Mass Spectrometry Data Analysis in Proteomics by Rune Matthiesen Pdf

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.

Proteomics for Biological Discovery

Timothy D. Veenstra,John R. Yates, III
Proteomics for Biological Discovery Book PDF

Author : Timothy D. Veenstra,John R. Yates, III
Publisher : John Wiley & Sons
Page : 361 pages
File Size : 42,6 Mb
Release : 2006-06-12
Category : Science
ISBN : 9780470007730

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Proteomics for Biological Discovery by Timothy D. Veenstra,John R. Yates, III Pdf

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.

Proteomic Profiling and Analytical Chemistry

Pawel Ciborowski,Jerzy Silberring
Proteomic Profiling and Analytical Chemistry Book PDF

Author : Pawel Ciborowski,Jerzy Silberring
Publisher : Elsevier
Page : 298 pages
File Size : 49,9 Mb
Release : 2016-03-02
Category : Science
ISBN : 9780444636904

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Proteomic Profiling and Analytical Chemistry by Pawel Ciborowski,Jerzy Silberring Pdf

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 and Metabolomic Approaches to Biomarker Discovery

Haleem J. Issaq,Timothy D. Veenstra
Proteomic and Metabolomic Approaches to Biomarker Discovery Book PDF

Author : Haleem J. Issaq,Timothy D. Veenstra
Publisher : Academic Press
Page : 504 pages
File Size : 45,5 Mb
Release : 2019-10-24
Category : Science
ISBN : 9780128197882

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Proteomic and Metabolomic Approaches to Biomarker Discovery by Haleem J. Issaq,Timothy D. Veenstra Pdf

Proteomic and Metabolomic Approaches to Biomarker Discovery, Second Edition 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. This second edition has been fully updated and revised to address recent advances in MS and NMR instrumentation, high-field NMR, proteomics and metabolomics for biomarker validation, clinical assays of biomarkers and clinical MS and NMR, identifying microRNAs and autoantibodies as biomarkers, MRM-MS assay development, top-down MS, glycosylation-based serum biomarkers, cell surface proteins in biomarker discovery, lipodomics for cancer biomarker discovery, and strategies to design studies to identify predictive biomarkers in cancer research. Addresses the full range of proteomic and metabolomic methods and technologies used for biomarker discovery and validation Covers all steps involved in biomarker discovery, from study design to study execution Serves as a vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals and graduate students

Subcellular Proteomics

Eric Bertrand,Michel Faupel
Subcellular Proteomics Book PDF

Author : Eric Bertrand,Michel Faupel
Publisher : Springer Science & Business Media
Page : 390 pages
File Size : 55,9 Mb
Release : 2007-08-29
Category : Science
ISBN : 9781402059438

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Subcellular Proteomics by Eric Bertrand,Michel Faupel Pdf

This volume summarizes the new developments that made subcellular proteomics a rapidly expanding area. It examines the different levels of subcellular organization and their specific methodologies. In addition, the book includes coverage of systems biology that deals with the integration of the data derived from these different levels to produce a synthetic description of the cell as a system.