Application Of Selected Reaction Monitoring To Highly Multiplexed Targeted Quantitative Proteomics

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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 : 46,7 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. ​

Recent Advances in Proteomics Research

Sameh Magdeldin
Recent Advances in Proteomics Research Book PDF

Author : Sameh Magdeldin
Publisher : BoD – Books on Demand
Page : 168 pages
File Size : 42,6 Mb
Release : 2015-11-11
Category : Science
ISBN : 9789535122012

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Recent Advances in Proteomics Research by Sameh Magdeldin Pdf

Proteomics refers to the entire complement of proteins, including modification. This promising discipline has enabled us to study proteins from a massive and comprehensive point of view. The book Recent Advances in Proteomics Research describes in five sections some of the applications of proteomics. This fine research has been written by leading experts worldwide. This book is aimed mainly at those interested in proteins and in the field of proteins, particularly biochemists, biologists, pharmacists, advanced graduate students and postgraduate researchers.

Multiplex Biomarker Techniques

Paul C. Guest
Multiplex Biomarker Techniques Book PDF

Author : Paul C. Guest
Publisher : Humana
Page : 0 pages
File Size : 48,8 Mb
Release : 2016-11-29
Category : Medical
ISBN : 1493967290

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Multiplex Biomarker Techniques by Paul C. Guest Pdf

This detailed book arrives as there is an increasing need for multiplex biomarker readouts for improved clinical management and to support the development of new drugs by pharmaceutical companies, due to continuous technical developments and new insights into the high complexity of many diseases. Chapters explore the basic technology platforms being applied in the fields of genomics, proteomics, transcriptomics, metabolomics, and imaging, which are currently the methods of choice in multiplex biomarker research. The book also describes the chief medical areas in which the greatest progress has been made and highlight areas where further resources are required. Written for the highly successful Methods in Molecular Biology series, methodology 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 invaluable, iMultiplex Biomarker Techniques: Methods and Applications

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 : 48,9 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

Handbook of Biomarkers and Precision Medicine

Claudio Carini,Mark Fidock,Alain van Gool
Handbook of Biomarkers and Precision Medicine Book PDF

Author : Claudio Carini,Mark Fidock,Alain van Gool
Publisher : CRC Press
Page : 631 pages
File Size : 53,6 Mb
Release : 2019-04-16
Category : Mathematics
ISBN : 9780429576737

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Handbook of Biomarkers and Precision Medicine by Claudio Carini,Mark Fidock,Alain van Gool Pdf

"The field of Biomarkers and Precision Medicine in drug development is rapidly evolving and this book presents a snapshot of exciting new approaches. By presenting a wide range of biomarker applications, discussed by knowledgeable and experienced scientists, readers will develop an appreciation of the scope and breadth of biomarker knowledge and find examples that will help them in their own work." -Maria Freire, Foundation for the National Institutes of Health Handbook of Biomarkers and Precision Medicine provides comprehensive insights into biomarker discovery and development which has driven the new era of Precision Medicine. A wide variety of renowned experts from government, academia, teaching hospitals, biotechnology and pharmaceutical companies share best practices, examples and exciting new developments. The handbook aims to provide in-depth knowledge to research scientists, students and decision makers engaged in Biomarker and Precision Medicine-centric drug development. Features: Detailed insights into biomarker discovery, validation and diagnostic development with implementation strategies Lessons-learned from successful Precision Medicine case studies A variety of exciting and emerging biomarker technologies The next frontiers and future challenges of biomarkers in Precision Medicine Claudio Carini, Mark Fidock and Alain van Gool are internationally recognized as scientific leaders in Biomarkers and Precision Medicine. They have worked for decades in academia and pharmaceutical industry in EU, USA and Asia. Currently, Dr. Carini is Honorary Faculty at Kings’s College School of Medicine, London, UK. Dr. Fidock is Vice President of Precision Medicine Laboratories at AstraZeneca, Cambridge, UK. Prof.dr. van Gool is Head Translational Metabolic Laboratory at Radboud university medical school, Nijmegen, NL.

Sample Preparation in Biological Mass Spectrometry

Alexander R. Ivanov,Alexander V. Lazarev
Sample Preparation in Biological Mass Spectrometry Book PDF

Author : Alexander R. Ivanov,Alexander V. Lazarev
Publisher : Springer
Page : 1089 pages
File Size : 43,8 Mb
Release : 2013-01-02
Category : Science
ISBN : 9400708297

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Sample Preparation in Biological Mass Spectrometry by Alexander R. Ivanov,Alexander V. Lazarev Pdf

The aim of this book is to provide the researcher with important sample preparation strategies in a wide variety of analyte molecules, specimens, methods, and biological applications requiring mass spectrometric analysis as a detection end-point. In this volume we have compiled the contributions from several laboratories which are employing mass spectrometry for biological analysis. With the latest inventions and introduction of highly sophisticated mass spectrometry equipment sample preparation becomes an extremely important bottleneck of biomedical analysis. We have a goal of giving the reader several successful examples of sample preparation, development and optimization, leading to the success in analytical steps and proper conclusions made at the end of the day. This book is structured as a compilation of contributed chapters ranging from protocols to research articles and reviews. The main philosophy of this volume is that sample preparation methods have to be optimized and validated for every project, for every sample type and for every downstream analytical technique.

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 : 50,8 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.

Targeted Biomarker Quantitation by LC-MS

Naidong Weng,Wenying Jian
Targeted Biomarker Quantitation by LC MS Book PDF

Author : Naidong Weng,Wenying Jian
Publisher : John Wiley & Sons
Page : 397 pages
File Size : 51,6 Mb
Release : 2017-07-31
Category : Medical
ISBN : 9781119103066

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Targeted Biomarker Quantitation by LC-MS by Naidong Weng,Wenying Jian Pdf

The first book to offer a blueprint for overcoming the challenges to successfully quantifying biomarkers in living organisms The demand among scientists and clinicians for targeted quantitation experiments has experienced explosive growth in recent years. While there are a few books dedicated to bioanalysis and biomarkers in general, until now there were none devoted exclusively to addressing critical issues surrounding this area of intense research. Target Biomarker Quantitation by LC-MS provides a detailed blueprint for quantifying biomarkers in biological systems. It uses numerous real-world cases to exemplify key concepts, all of which were carefully selected and presented so as to allow the concepts they embody to be easily expanded to future applications, including new biomarker development. Target Biomarker Quantitation by LC-MS primarily focuses on the assay establishment for biomarker quantitation—a critical issue rarely treated in depth. It offers comprehensive coverage of three core areas of biomarker assay establishment: the relationship between the measured biomarkers and their intended usage; contemporary regulatory requirements for biomarker assays (a thorough understanding of which is essential to producing a successful and defendable submission); and the technical challenges of analyzing biomarkers produced inside a living organism or cell. Covers the theory of and applications for state-of-the-art mass spectrometry and chromatography and their applications in biomarker analysis Features real-life examples illustrating the challenges involved in target biomarker quantitation and the innovative approaches which have been used to overcome those challenges Addresses potential obstacles to obtain effective biomarker level and data interpretation, such as specificity establishment and sample collection Outlines a tiered approach and fit-for-purpose assay protocol for target biomarker quantitation Highlights the current state of the biomarker regulatory environment and protocol standards Target Biomarker Quantitation by LC-MS is a valuable resource for bioanalytical scientists, drug metabolism and pharmacokinetics scientists, clinical scientists, analytical chemists, and others for whom biomarker quantitation is an important tool of the trade. It also functions as an excellent text for graduate courses in pharmaceutical, biochemistry and chemistry.

The Science and Regulations of Naturally Derived Complex Drugs

Ram Sasisekharan,Sau L. Lee,Amy Rosenberg,Larry A. Walker
The Science and Regulations of Naturally Derived Complex Drugs Book PDF

Author : Ram Sasisekharan,Sau L. Lee,Amy Rosenberg,Larry A. Walker
Publisher : Springer
Page : 331 pages
File Size : 40,6 Mb
Release : 2019-04-23
Category : Medical
ISBN : 9783030117511

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The Science and Regulations of Naturally Derived Complex Drugs by Ram Sasisekharan,Sau L. Lee,Amy Rosenberg,Larry A. Walker Pdf

This volume in the AAPS Advances series covers various quality, safety and clinical aspects of drug development that are relevant to new and/or generic drugs containing a complex mixture of molecules. Specific topics discussed include: raw materials sourcing; manufacturing controls; characterization; identification of critical product quality components and attributes; identification of impurities, particularly as they bear on toxicity and immunogenicity; clinical trial study design considerations, and the regulatory science applications to development of such complex mixtures. Complex mixtures are challenging to characterize and analyze using standard methods. Further challenges extend throughout the product development cycle from raw material control to clinical study design. The regulatory landscape is rapidly changing as new types of complex mixtures are introduced into clinical trials and to the market (e.g., traditional Chinese medicines and medical marijuana products), while older products are facing generic competition for the first time (e.g., enoxaparin). The future outlook for complex generic drug products, as opposed to the more commonly developed targeted single agent drug products is not clear. The risks pertaining to lack of a full understanding of raw material control, process and controls in manufacture, as well as characterization of a complex mixture were seen vividly during the heparin crisis of 2008. As such powerful lessons have been learned about the regulatory science specific to complex products. The Science and Regulations of Naturally Derived Complex Drugs addresses the interests among industry, academics, and government on the issues surrounding the future development of mixtures for medicinal use.

General Methods in Biomarker Research and their Applications

Victor R. Preedy,Vinood B. Patel
General Methods in Biomarker Research and their Applications Book PDF

Author : Victor R. Preedy,Vinood B. Patel
Publisher : Springer
Page : 0 pages
File Size : 40,9 Mb
Release : 2015-08-14
Category : Medical
ISBN : 9400776950

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General Methods in Biomarker Research and their Applications by Victor R. Preedy,Vinood B. Patel Pdf

In the past decade there has been a major sea change in the way disease is diagnosed and investigated due to the advent of high throughput technologies, such as microarrays, lab on a chip, proteomics, genomics, lipomics, metabolomics etc. These advances have enabled the discovery of new and novel markers of disease relating to autoimmune disorders, cancers, endocrine diseases, genetic disorders, sensory damage, intestinal diseases etc. In many instances these developments have gone hand in hand with the discovery of biomarkers elucidated via traditional or conventional methods, such as histopathology or clinical biochemistry. Together with microprocessor-based data analysis, advanced statistics and bioinformatics these markers have been used to identify individuals with active disease or pathology as well as those who are refractory or have distinguishing pathologies. New analytical methods that have been used to identify markers of disease and is suggested that there may be as many as 40 different platforms. Unfortunately techniques and methods have not been readily transferable to other disease states and sometimes diagnosis still relies on single analytes rather than a cohort of markers. There is thus a demand for a comprehensive and focused evidenced-based text and scientific literature that addresses these issues. Hence the formulation of Biomarkers in Disease. The series covers a wide number of areas including for example, nutrition, cancer, endocrinology, cardiology, addictions, immunology, birth defects, genetics and so on. The chapters are written by national or international experts and specialists.

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 : 53,5 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

Foodomics

Jorge Barros-Velázquez
Foodomics Book PDF

Author : Jorge Barros-Velázquez
Publisher : Royal Society of Chemistry
Page : 515 pages
File Size : 48,5 Mb
Release : 2021-03-31
Category : Science
ISBN : 9781788018845

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Foodomics by Jorge Barros-Velázquez Pdf

Presents the most updated information on the main methodologies and technological platforms involved in foodomics.

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 : 40,5 Mb
Release : 2019-07-10
Category : Science
ISBN : 9781118970218

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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.

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 : 40,6 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.

Quantitative Methods in Proteomics

Katrin Marcus
Quantitative Methods in Proteomics Book PDF

Author : Katrin Marcus
Publisher : Humana Press
Page : 539 pages
File Size : 49,9 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.