Development And Application Of Comparative Proteomics And Glycoproteomics Approaches Based On Liquid Phase Separation And Mass Spectrometry
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Development And Application Of Comparative Proteomics And Glycoproteomics Approaches Based On Liquid Phase Separation And Mass Spectrometry
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Author : Jia Zhao
language : en
Publisher:
Release Date : 2007
Development And Application Of Comparative Proteomics And Glycoproteomics Approaches Based On Liquid Phase Separation And Mass Spectrometry written by Jia Zhao and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with categories.
Essentials Of Glycobiology
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Author : Ajit Varki
language : en
Publisher: CSHL Press
Release Date : 1999
Essentials Of Glycobiology written by Ajit Varki and has been published by CSHL Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1999 with Medical categories.
Sugar chains (glycans) are often attached to proteins and lipids and have multiple roles in the organization and function of all organisms. "Essentials of Glycobiology" describes their biogenesis and function and offers a useful gateway to the understanding of glycans.
Mass Spectrometry Based Glycoproteomics And Its Clinic Application
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Author : Haojie Lu
language : en
Publisher:
Release Date : 2023-09-25
Mass Spectrometry Based Glycoproteomics And Its Clinic Application written by Haojie Lu and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-09-25 with Glycoproteins categories.
This book demonstrates the progress that has been achieved in Mass spectrometry based glycoproteomic analysis, including a wide range of analytical methodologies and strategies involved in selective enrichment, qualitative analysis, quantitative analysis and data analysis, together with their clinical applications.
Mass Spectrometry Based Chemical Proteomics
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Author : W. Andy Tao
language : en
Publisher: John Wiley & Sons
Release Date : 2019-07-10
Mass Spectrometry Based Chemical Proteomics written by W. Andy Tao and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-07-10 with Science categories.
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.
Novel Data Analysis Approaches For Cross Linking Mass Spectrometry Proteomics And Glycoproteomics
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Author : Lei Lu
language : en
Publisher:
Release Date : 2021
Novel Data Analysis Approaches For Cross Linking Mass Spectrometry Proteomics And Glycoproteomics written by Lei Lu and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.
Bottom-up proteomics has emerged as a powerful technology for biological studies. The technique is used for a myriad of purposes, including among others protein identification, post-translational modification identification, protein-protein interaction analysis, protein quantification analysis, and protein structure analysis. The data analysis approaches of bottom-up proteomics have evolved over the past two decades, and many different algorithms and software programs have been developed for these varied purposes. In this thesis, I have focused on improving the database search strategies for the important special applications of bottom-up proteomics, including cross-linking mass spectrometry proteomics and O-glycoproteomics. In cross-linking mass spectrometry proteomics, a sample of proteins is treated with a chemical cross-linking reagent. This causes peptides within the proteins to be cross-linked to one another, forming peptide doublets that are released by treatment of the sample with a protease such as trypsin. The data analysis tools are designed to identify the cross-linked peptides. In O-glycoproteomics, the peptides that are released by protease digestion of the protein sample can be modified with any of or even multiple distinct O-glycans, and the data analysis tools should be able to identify all of the glycans and the modification sites at which they are located. In both cases, traditional database searching strategies which try to match the experimental spectra to all potential theoretical spectra is not practical due to the large increases in search space. Researchers suffered from a lack of efficient data analysis tools for these two applications. Here we successfully devised new search algorithms to address these problems, and impemented them in two new software modules in our laboratories' bottom-up software engine MetaMorpheus (Crosslinking data analysis via MetaMorpheusXL and O-glycoproteomics data analysis via O-Pair Search). The new search strategies used in the software program are both based on ion-indexed open search, which was first developed for large scale proteomic studies in the programs MSFragger and Open-pFind. The ion-indexed open search was optimized for cross-linking mass spectrometry proteomics and O-glycoproteomics in this study, and combined with other algorithms. In O-glycoproteomics, a graph-based algorithm is used to speed up the identification and localization of O-glycans. Other useful features have been added in the software program, such as enabling analysis of both cleavable cross-links and non-cleavable cross-links in the cross-link search module, and calculating localization probabilities in the O-glyco search module. Further optimizations including machine learning methods for false discovery rate (FDR) analysis, retention time prediction and spectral prediction could further improve the current best search approaches for cross-link proteomics and O-glycoproteomics data analysis. Chapter 1 provides an overview of bottom-up proteomics data analysis methods and outlines how ion-indexed open search could be useful for special bottom-up proteomics studies. Chapter 2 describes the development of a cross-linking mass spectrometry proteomics search module, resulting in efficiency improvements for both cleavable and non-cleavable cross-link proteomics data analysis. Chapter 3 describes the development of an O-glycoproteomics search module; by combining the ion-indexed open search algorithm with the graph-based localization algorithm, the O-pair Search is more than 2000 times faster than the currently widely used software program Byonic. In Chapter 4, a novel top-down data acquisition method is described. Chapter 5 provides conclusions and future directions.
Proteomics For Biological Discovery
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Author : Timothy D. Veenstra
language : en
Publisher: John Wiley & Sons
Release Date : 2006-06-12
Proteomics For Biological Discovery written by Timothy D. Veenstra and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-06-12 with Science categories.
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.
Separation Methods In Proteomics
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Author : Gary B. Smejkal
language : en
Publisher: CRC Press
Release Date : 2005-12-12
Separation Methods In Proteomics written by Gary B. Smejkal and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-12-12 with Medical categories.
Driven by the widespread growth of proteomic practices, protein separation techniques have been refined to minimize variability, optimize particular applications, and adapt to user preferences in the analysis of proteins. Separation Methods in Proteomics provides a comprehensive examination of all major separation techniques for proteomic
Proteome Analysis
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Author : David W Speicher
language : en
Publisher: Elsevier
Release Date : 2004-05-18
Proteome Analysis written by David W Speicher and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004-05-18 with Science categories.
This book explores the current status of proteomics, an exciting new discipline, which is less than 10 years old. This new field has rapidly grown into a major commercial and research enterprise with great prospects for dramatically advancing our knowledge of basic biological and disease processes. The contributors to this book are an international panel of proteomics experts, who review and discuss the current status of specific technologies and approaches. Proteomics represents an exciting new way to pursue biological and biomedical science at an unprecedented pace. Proteomics takes a broad, comprehensive, systematic approach to understanding biology that is generally unbiased and not dependent upon existing knowledge. The major components of proteomics from basic discovery using a range of alternative analytical methods to discovery validation and use for clinical applications are discussed. State-of-the-art protein profiling methods include high resolution two-dimensional gels, two-dimensional differential in-gel electrophoresis, LC-MS and LC-MS/MS using accurate mass tags, and protein identifications of proteins from gels using mass spectrometry methods are discussed in depth. Other chapters describe comprehensive characterization of proteomes using electrophoretic prefractionation and analyses of sub-proteomes based on specific posttranslational modifications including the phospho-proteome, the glyco-proteome, and nitrated proteins. These conventional proteome analysis chapters are complemented by discussion of emerging technologies and approaches such as affinity based biosensor proteomics as well as the use of protein microarrays, microfluidics and nanotechnology. Strategies for improving throughput by automation are also discussed. Additional chapters address the application of current proteome techniques to clinical problems and the availability of protein expression library resources for proteome studies. · Authored by international experts in the field · Covers a wide range of topics including 2-D gels, global proteomics using accurate mass tags, global proteomics using electrophoretic prefractionation, microfluidics, and nanotechnology · Includes state-of-the-art protein profiling methods, and emerging technologies
Advances In Carbohydrate Chemistry And Biochemistry
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Author :
language : en
Publisher: Academic Press
Release Date : 2017-11-23
Advances In Carbohydrate Chemistry And Biochemistry written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-11-23 with Science categories.
Advances in Carbohydrate Chemistry and Biochemistry, Volume 74, presents a definitive interpretation of the current status and future trends in carbohydrate chemistry and biochemistry. Since its inception in 1945, the series has provided critical and informative articles written by research specialists that integrate the industrial, analytical and technological aspects of biochemistry, organic chemistry and instrumentation methodology to the study of carbohydrates. Features contributions from leading authorities and industry experts who specialize in carbohydrate chemistry, biochemistry and research Integrates the industrial, analytical and technological aspects of biochemistry, organic chemistry and instrumentation methodology in the study of carbohydrates Informs and updates on all the latest developments in the field
The Glycome
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Author : Adeel Malik
language : en
Publisher: CRC Press
Release Date : 2021-07-07
The Glycome written by Adeel Malik and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-07-07 with Science categories.
This volume provides a comprehensive understanding of the enigmatic identity of the glycome, a complex but important area of research that has been largely ignored due to its complexity. The authors thoroughly deal with almost all aspects of the glycome, i.e., elucidation of the glycan identity enigma and its role in regulation of the cellular process, and in disease etiology. The book bridges the knowledge gap in understanding the glycome, from being a cell signature to its applications in disease etiology. In addition, it details many of the major insights regarding the possible role of the glycome in various diseases as a therapeutic marker. The book systematically covers the major aspects of the glycome, including the significance of substituting the diverse monosaccharide units to glycoproteins, the role of glycans in disease pathologies, and the challenges and advances in glycobiology. The authors stress the significance and huge encoding power of carbohydrates as well as provide helpful insights in framing the bigger picture. The Glycome: Understanding the Diversity and Complexity of Glycobiology details state-of-the-art developments and emerging challenges of glycome biology, which are going to be key areas of future research, not only in the glycobiology field but also in pharmaceutics.