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Mass Spectrometry Based Structural Proteomics
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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
Book Synopsis Mass Spectrometry-Based Proteomics by : Kris Gevaert
Download or read book Mass Spectrometry-Based Proteomics written by Kris Gevaert and published by Springer Nature. This book was released on 2023-09-04 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume explores contemporary techniques in mass spectrometry-based proteomics. After covering overall proteome coverage and the cellular surfaceome, the book delves into proximity-induced biotinylation, abduction of protein complexes in viral-like particles, and thermal proteome profiling, as well as protocols for identifying protein N-terminal acetylation, protein processing by proteases, protein N-glycosylation, and protein phosphorylation. The book also collects chapters on automated preparation of clinical samples, the analysis of formalin-fixed paraffin-embedded samples, protocols for the isolation of extracellular vesicles and for the monitoring of selected protein modifications in clinical samples, and, finally, structural proteomics. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Mass Spectrometry-Based Proteomics serves as an ideal guide to its subject for both novices in the field of proteomics as well as specialists.
Book Synopsis Spectral Techniques In Proteomics by : Daniel S. Sem
Download or read book Spectral Techniques In Proteomics written by Daniel S. Sem and published by CRC Press. This book was released on 2007-03-30 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Facilitating the innovation, development, and application of new spectroscopic methods in proteomics, Spectral Techniques in Proteomics provides a broad overview of the spectroscopic toolbox that can be used, either with proteome or sub-proteome mixtures or with individual/purified proteins studied in parallel. It gives a modest overview of
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 2019-09-04 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.
Book Synopsis Principles of Proteomics by : Richard Twyman
Download or read book Principles of Proteomics written by Richard Twyman and published by Taylor & Francis. This book was released on 2004-06-02 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: Principles of Proteomics provides a comprehensive introduction to this relatively new field, for the first time bringing together all the disparate themes of proteomics.
Book Synopsis Development and Application of Mass Spectrometry-based Protein Footprinting in Structural Proteomics by : Ming Cheng (Chemist)
Download or read book Development and Application of Mass Spectrometry-based Protein Footprinting in Structural Proteomics written by Ming Cheng (Chemist) and published by . This book was released on 2019 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integral mass spectrometry (MS) has emerged as an important tool for protein structural characterization. It readouts are a broad range of structural information, including stoichiometry, interactions, conformations and conformation change, and dynamics. Protein footprinting is a pivotal component in the intergral MS toolkit.My dissertation centers around the development and application of protein footprinting to characterize protein structure. It is divided into seven chapters. Chapter 1 serves as the introduction for integral mass spectrometry in structural proteomic. In Chapter 2, we extended the fast-photochemical oxidation of proteins (FPOP) platform by adding the trifluoromethyl radical (·CF3) as a new reagent. We discovered that ·CF3 footprint proteins in a complementary way as hydroxide radicals. The ·CF3 radical has exceptional reactivity, modifying 18 amino acids out of 20. Further studies demonstrate that it can report the conformational change between holo-myoglobin and apo-myoglobin and can define the topology of the VKOR membrane protein. This work bridges trifluoromethylation chemistry in materials and medicinal chemistry to that in structural biology. In Chapter 3, collaborated with Dr. Mark Chance's laboratory in Case Western Reserve University (CWRU) to apply ·CF3 chemistry on the synchrotron platform, which is the first platform that uses ·OH for protein footprinting. Synchrotron radiolysis generates ·CF3 in water media by ionizing water molecules to give ·OH. The ·CF3 shows complementary chemical reactivity with canonical ·OH labeling yet results in higher reactivity coverage. The ·CF3 reagent is the second footprinting reagent enabled by synchrotron since 1999. This work serves as a proof-of-concept to demonstrate that synchrotron platform is adaptable to other novel chemistries that can increase footprinting coverage. Further, taking advantage of X-ray irradiation, we achieved direct protein trifluoromethylation in the absence of metal catalysis or peroxide for the first time, with the synchrotron platform. In Chapter 4, we devloped a laser-mediated radical method for integral membrane protein (IMP) footprinting. Classical footprinting methods use hydrophilic reagents to label protein surfaces. IN so doing, we generate structural information by measuring the solvent accessibility of the backbone or side chains in aqueous media. Owing to the amphipathic nature of IMP, this new approach exploits the highly hydrophobic nature of perfluoroalkyl iodine together with tip sonication to ensure efficient labeling of a transmembrane domain (TM). The chemistry yields 100% reactivity coverage for tyrosine, and complete IMP labeling in a fast fashion. The resulting protein modification, which is resistant to hydrolysis, compatible with proteolysis, and amenable of tandem mass analysis, is appropriate for footprinting by bottom-up analysis. (Collaboration with Dr. Weikai Li from Wash U Medical School). In Chapter 5, we investigated an array of digestion conditions by using different combination of protease and additives to optimize the coverage of IMP digestion. IMPs are under-represented in conventional bottom-up proteomic analysis that generally favors soluble, abundant and easy-to-digest proteins. The new protrocol of IMP digestion significantly decreases our workload for sample preparation, allows us to avoid common contaminants that impair LC-MS, and generally yields >90% sequence coverage by generating peptides suitable for structural proteomic studies. Further, the deep analysis enable us to identify a "sweet spot" in the digestion protocol that may provide guidance to choose a suitable protease in structural proteomics in future. In Chapter 6, apart from methodology development, we used hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize the binding interface for Mxra8-immune complex and Mxra8-chikungunya virus protein complex. The cell adhesion molecule Mxra8 is identified as a receptor for multiple arthritogenic alphaviruses such as chikungunya virus. We identified putative binding sites for eight anti-Mxra8 monoclonal antibodies (mAbs). HDX-MS enables us to classify the novel mAbs, predict their competing binding interface with chikungunya virus, and provide a molecular level explanation for the observation that mAbs can block the Chikungunya virus infection. From the HDX kinetic curves, we also observe that the mAbs have higher affinity than do Chikungunya virus proteins when binding with Mxa8. Finally, the HDX data help to assign the orientation of Mxra8 on the Cryo-EM structure of Chikungunya virus complex (Collaboration with Dr. Daved H. Fremont and Dr. Michael s Diamond, Wash U School of Medicine). In Chapter 7, we provide a conclusion for my dissertation. We will discuss challenges and opportunities for protein footprinting, and its role in the expanding toolkit of structural proteomics.
Book Synopsis Methods in Proteome and Protein Analysis by : Roza Maria Kamp
Download or read book Methods in Proteome and Protein Analysis written by Roza Maria Kamp and published by Springer Science & Business Media. This book was released on 2004-01-23 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Following the succesful publication of "Proteome and Protein Analysis" in 2000, which was based on a former MPSA (Methods in Protein Structure Analysis) conference, "Methods in Proteome and Protein Analysis" presents the most interesting papers from the 14th MPSA meeting. Major topics include: X-ray crystallography, mass spectrometry or cryo-electron microscopy tomography and different experimental approaches for the study of very large multi-subunit molecular nanomaschines; development of high throughput methods for large-scale protein expression and purification and automatic data acquisition for structure determination by both X-ray diffraction and NMR spectroscopy; mechanisms of protein folding and misfolding in vitro and in vivo; protein-protein interactions; analysis of post-translational modifications; the classification, prediction of structure or functional sites, and evolution of protein folds and functions. TOC: Includes 25 chapters organized in the following parts: Structural Proteomics Proteome Analysis Structure-Function Correlations Protein-Protein Interaction Advanced Technologies Protein Sequencing and Amino Acids Analysis Bioinformatics
Book Synopsis Mass Spectrometry in Structural Biology and Biophysics by : Igor A. Kaltashov
Download or read book Mass Spectrometry in Structural Biology and Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2012-03-02 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biology, and biopharmaceuticals, the book is a practical guide to understanding the role of MS techniques in biophysical research. Designed to meet the needs of both academic and industrial researchers, it makes mass spectrometry accessible to professionals in a range of fields, including biopharmaceuticals. This new edition has been significantly expanded and updated to include the most recent experimental methodologies and techniques, MS applications in biophysics and structural biology, methods for studying higher order structure and dynamics of proteins, an examination of other biopolymers and synthetic polymers, such as nucleic acids and oligosaccharides, and much more. Featuring high-quality illustrations that illuminate the concepts described in the text, as well as extensive references that enable the reader to pursue further study, Mass Spectrometry in Structural Biology and Biophysics is an indispensable resource for researchers and graduate students working in biophysics, structural biology, protein chemistry, and related fields.
Book Synopsis Structural Proteomics and Its Impact on the Life Sciences by : Joel Sussman
Download or read book Structural Proteomics and Its Impact on the Life Sciences written by Joel Sussman and published by World Scientific. This book was released on 2008 with total page 597 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ranging from policy issues related to funding and goals, through high-throughput procedures for protein production, this text presents an overview of structural proteomics via a multidisciplinary approach involving molecular biology.
Book Synopsis Computational and Statistical Methods for Protein Quantification by Mass Spectrometry by : Ingvar Eidhammer
Download or read book Computational and Statistical Methods for Protein Quantification by Mass Spectrometry written by Ingvar Eidhammer and published by John Wiley & Sons. This book was released on 2012-12-10 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Mass Spectrometry-based Structural Proteomics by : Ben Niu (Chemist)
Download or read book Mass Spectrometry-based Structural Proteomics written by Ben Niu (Chemist) and published by . This book was released on 2017 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: The dissertation will be solely focused on using mass spectrometry to characterize protein high order structures (HOS), it emphasizes the use of hydroxyl radical footprinting (FPOP) coupled to bottom-up MS approach. A detailed background information about FPOP, and the corresponding method developments as well as applications will be covered.The first chapter will be a comprehensive review regarding the FPOP. Following this, chapter 2, 3, and 4 will be focused on the method developments. Chapter 2 describes an isotope dilution GC-MS method to quantitate OH radicals in FPOP; chapter 3 describes the incorporation of Leu-enkephalin as reporter peptide for a more quantitative FPOP platform; and chapter 4 introduces how R-programming can facilitate the MS-based structural proteomics. After this, chapter 5, 6, and 7 are mainly about the applications of FPOP to characterize the proteins. Chapter 5 talks about using FPOP to localize the dimer dissociation and local unfolding of G93A SOD1; chapter 6 describes how FPOP can be used to characterize an intrinsically disordered tail of EGF receptor protein; and chapter 7 demonstrates the feasibility of a marriage of FPOP and Nanodiscs to study the membrane-associated KRAS protein.
Book Synopsis Mass Spectrometry–Based Glycoproteomics and Its Clinic Application by : Haojie Lu
Download or read book Mass Spectrometry–Based Glycoproteomics and Its Clinic Application written by Haojie Lu and published by CRC Press. This book was released on 2021-09-21 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: As one of the most extensive and important protein post-translational modifications, glycosylation plays a vital role in regulating organisms and is associated with various physiological and pathological processes. Recently, researchers have focused on the need to characterize protein glycosylation sites, structures, and their degree of modification, to better understand their biological functions while also looking for potential biomarkers for diagnosis and treatment of disease. Mass spectrometry (MS) is one of the most powerful tools used to study biomolecules including glycoproteins and glycans. With the continuous development of glycoproteomics and glycomics based on MS analysis, more techniques have evolved and contribute to understanding the structure and function of glycoproteins and glycans. This book reviews advancements achieved in MS-based glycoproteomic analysis, including a wide range of analytical methodologies and strategies involved in selective enrichment; as well as qualitative, quantitative, and data analysis, together with their clinical applications. Significant examples are discussed to illustrate the principles, laboratory protocols, and advice for key implementation to ensure successful results. Mass Spectrometry–Based Glycoproteomics and Its Clinic Application will serve as a valuable resource to elucidate new techniques and their applications for students, postdocs, and researchers working in proteomics, glycoscience, analytical chemistry, biochemistry, and clinical medicine. Editor: Haojie Lu is a professor at Fudan University, specializing in proteomics based on mass spectrometry with particular emphasis on novel technologies for separation and identification of low-abundant proteins and post-translationally modified proteins (including glycosylation), as well as relative and absolute quantification methods for proteomics.
Book Synopsis Mass Spectrometry Structural Proteomics by : Giuseppe Infusini
Download or read book Mass Spectrometry Structural Proteomics written by Giuseppe Infusini and published by . This book was released on 2005 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Proteomics for Biological Discovery by : Timothy D. Veenstra
Download or read book Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2019-07-18 with total page 363 pages. Available in PDF, EPUB and Kindle. Book excerpt: An update to the popular guide to proteomics technology applications in biomedical research Building on the strength of the original edition, this book presents the state of the art in the field of proteomics and offers students and scientists new tools and techniques to advance their own research. Written by leading experts in the field, it provides readers with an understanding of new and emerging directions for proteomics research and applications. Proteomics for Biological Discovery begins by discussing the emergence of proteomics technologies and summarizing the potential insights to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are thoroughly covered, from underlying concepts to limitations and future directions. Later chapters provide an overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, applied proteomics, and bioinformatics relevant to proteomics. Chapters cover: Quantitative Proteomics for Differential Protein Expression Profiling; Protein Microarrays; Protein Biomarker Discovery; Biomarker Discovery using Mass Spectrometry Imaging; Protein-Protein Interactions; Mass Spectrometry Of Intact Protein Complexes; Crosslinking Applications in Structural Proteomics; Functional Proteomics; High Resolution Interrogation of Biological Systems via Mass Cytometry; Characterization of Drug-Protein Interactions by Chemoproteomics; Phosphorylation; Large-Scale Phosphoproteomics; and Probing Glycoforms of Individual Proteins Using Antibody-Lectin Sandwich Arrays. Presents a comprehensive and coherent review of the major issues in proteomic 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 Features new coverage of mass spectrometry for high throughput proteomic measurements, and novel quantitation strategies such as spectral counting and stable isotope labeling Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Offers new chapters on biomarker discovery, global phosphorylation analysis, proteomic profiling using antibodies, and single cell mass spectrometry Proteomics for Biological Discovery is an excellent advanced resource for graduate students, postdoctoral fellows, and scientists across all the major fields of biomedical science.
Book Synopsis Mass Spectrometry Based Single Cell Proteomics by : Ákos Végvári
Download or read book Mass Spectrometry Based Single Cell Proteomics written by Ákos Végvári and published by Springer Nature. This book was released on 2024 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the latest advancements made in the field of mass spectrometry (MS) based single cell proteomics. The chapters in this book focus on technologies, methods, and biological applications and together cover the entire single cell proteomics analysis workflow, from sample collection and preparation through liquid chromatographic separation and mass spectrometric data acquisition to data analysis and interpretation. 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. Cutting-edge and authoritative, Mass Spectrometry Based Single Cell Proteomics: Methods and Protocols is a valuable resource for all researchers interested in using these technologies and methods in their laboratories to continue making biological discoveries in this important field.
Book Synopsis Analysis of Protein Post-Translational Modifications by Mass Spectrometry by : John R. Griffiths
Download or read book Analysis of Protein Post-Translational Modifications by Mass Spectrometry written by John R. Griffiths and published by John Wiley & Sons. This book was released on 2016-11-07 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covers all major modifications, including phosphorylation, glycosylation, acetylation, ubiquitination, sulfonation and and glycation Discussion of the chemistry behind each modification, along with key methods and references Contributions from some of the leading researchers in the field A valuable reference source for all laboratories undertaking proteomics, mass spectrometry and post-translational modification research
Book Synopsis Mass Spectrometry in Biophysics by : Igor A. Kaltashov
Download or read book Mass Spectrometry in Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2005-05-06 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first systematic summary of biophysical mass spectrometrytechniques Recent advances in mass spectrometry (MS) have pushed the frontiersof analytical chemistry into the biophysical laboratory. As aresult, the biophysical community's acceptance of MS-based methods,used to study protein higher-order structure and dynamics, hasaccelerated the expansion of biophysical MS. Despite this growing trend, until now no single text has presentedthe full array of MS-based experimental techniques and strategiesfor biophysics. Mass Spectrometry in Biophysics expertly closesthis gap in the literature. Covering the theoretical background and technical aspects of eachmethod, this much-needed reference offers an unparalleled overviewof the current state of biophysical MS. Mass Spectrometry inBiophysics begins with a helpful discussion of general biophysicalconcepts and MS-related techniques. Subsequent chaptersaddress: * Modern spectrometric hardware * High-order structure and dynamics as probed by various MS-basedmethods * Techniques used to study structure and behavior of non-nativeprotein states that become populated under denaturingconditions * Kinetic aspects of protein folding and enzyme catalysis * MS-based methods used to extract quantitative information onprotein-ligand interactions * Relation of MS-based techniques to other experimental tools * Biomolecular properties in the gas phase Fully referenced and containing a helpful appendix on the physicsof electrospray mass spectrometry, Mass Spectrometry in Biophysicsalso offers a compelling look at the current challenges facingbiomolecular MS and the potential applications that will likelyshape its future.
