Download or read book Quantitative Characterization of Proteins and Post translational Modifications in Complex Proteomes Using High resolution Mass Spectrometry based Proteomics written by Zhou Li (Researcher in biological systems) and published by . This book was released on 2014 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry-based proteomics is focused on identifying the entire suite of proteins and their post-translational modifications (PTMs) in a cell, organism, or community. In particular, quantitative proteomics measures abundance changes of thousands of proteins among multiple samples and provides network-level insight into how biological systems respond to environmental perturbations. Various quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling. This dissertation starts with systematic comparison of these three methods, and shows that isobaric chemical labeling provides accurate, precise, and reproducible quantification for thousands of proteins. Based on these results, we applied this approach to characterizing the proteome of Arabidopsis seedlings treated with Strigolactones (SLs), a new class of plant hormones that modulate various developmental processes. Our study reveals that SLs regulate the expression of a range of proteins that have not been assigned to SL pathways, which provides novel targets for follow-up genetic and biochemical characterization of SL signaling. The same approach was also used to measure how elevated temperature impacts the physiology of individual microbial groups in an acid mine drainage (AMD) microbial community, and shows that related organisms differed in their abundance and functional responses to temperature. Elevated temperature repressed carbon fixation by two Leptospirillum genotypes, whereas carbon fixation was significantly up-regulated at higher temperature by a third member of this genus. Further, we developed a new proteomic approach that harnessed high-resolution mass spectrometry and supercomputing for direct identification and quantification of a broad range of PTMs from an AMD microbial community. We find that PTMs are extraordinarily diverse between different growth stages and highly divergent between closely related bacteria. The findings of this study motivate further investigation of the role of PTMs in the ecology and evolution of microbial communities. Finally, a computational approach has been developed to improve the sensitivity of phosphopeptide identification. Overall, the research presented in the dissertation not only reveals biological insights with existing quantitative proteomics methods, but also develops novel methodologies that open up new avenues in studying PTMs of proteins (e.g. PTM cross-talk).

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

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

Download or read book Mass Spectrometry Based Chemical Proteomics written by W. Andy Tao and published by John Wiley & Sons. This book was released on 2019-07-10 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.

Download or read book Quantitative Proteomics written by Claire E Eyers and published by Royal Society of Chemistry. This book was released on 2014-01-10 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Quantitative Proteomics by Mass Spectrometry written by Salvatore Sechi and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Proteome Characterization and Proteomics written by Timothy D. Veenstra and published by Academic Press. This book was released on 2003-10-01 with total page 445 pages. Available in PDF, EPUB and Kindle. Book excerpt: The content of this volume is designed to reach a wide audience, including those involved with relevant technologies such as electrophoresis and mass spectrometry, to those interested in how proteomics can benefit research. A wide range of techniques are discussed, each specifically designed to address different needs in proteomic analysis. The concluding chapter discusses the important issue related to handling large amounts of data accumulated in proteomic studies. Discusses proteomics in the postgenomic age Includes various strategies for quantitative proteomics Covers the role of MS in structural functional proteomics and proteomics in drug discovery and bioinformatics

Download or read book Proteome Analysis written by David W Speicher and published by Elsevier. This book was released on 2004-05-18 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Mass spectrometric Methods for Quantitative Proteomics and Post translational Modification Mapping written by Ievgen Motorykin and published by . This book was released on 2015 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: Signal transduction within and between cells is at the core of biological activity in all living systems. Signaling networks are required for regulating biological functions, including growth, development and survival. Deregulation of signaling cascades has been linked to chronic and acute diseases and disorders This thesis focuses on mass spectrometry as a high resolution and high mass accuracy technique for the detection and characterization of proteins in biological systems. The thesis presents applications of contemporary mass-spectrometric methods to identify proteins, determine changes in their expression levels, and characterize post-translational modifications, in an effort to study changes in cell signaling in response to stress or disease. Various sample preparation methods to successfully suit needs of different biological questions were developed and applied: (1) extraction of the proteome, (2) chemical tagging and enrichment of the ATPome, a sub proteome comprising nucleotide binding proteins in particularly ATP-binding proteins including kinases, and (3) metal affinity complexation and enrichment of phosphopeptides. We used the following hybrid mass analyzer configurations: a quadrupole time-of-flight (qToF) instrument with ion mobility, a linear ion trap hyphenated with a FT-ICR mass spectrometry (LTQ-FT) and a hybrid ion trap-orbitrap mass spectrometer (Orbitrap Elite). The bioinformatic analysis of the proteomics data required multiple combinations of software packages to sequence proteins, perform absolute and relative quantification, statistically analyze and visualize data. Chapter 3 describes the use of zebrafish (Danio rerio) as one of the few vertebrate models that similar to humans cannot synthesize vitamin C to investigate the system-wide consequences of deficiencies in two essential micronutrients, vitamins E and C, on the proteome biology. A label-free proteomics workflow was applied to detect changes in protein abundance estimates dependent on vitamin regimes. The study reveals suppression in an energy metabolism cycle, glycolysis, in vitamin C and E deficient zebrafish. It was discovered that alternative energy cycle, glutaminolysis, is activated to fulfill energy requirement. Chapter 4 focuses on the determination of proteome differences that can be linked to the propensity of metastasis in osteosarcoma (OS), a bone cancer that predominantly targets the adolescent age group. OS has a high propensity to metastasize to the lungs, which is associated with a poor prognosis. The study utilizes canine osteosarcoma cell lines that were originally obtained from orthotropic primary OS and metastatic cells. Canis familiaris, the domestic dog, is an established large animal model of OS that recapitulate many biological and clinical features of the human malignancy. We applied a two-prone comparative proteomics approach that consisted of: (a) determination of protein abundance levels and (b) focus on kinases, a functional sub-proteome, using a chemical affinity tag for enrichment of ATP-binding proteins. Findings of this study indicated that in the highly metastasizing canine osteosarcoma cell line proteins associated with extracellular adhesion were deregulated, which may enhance metastogenesis. Mitogen activated protein kinases MAP2K6, MAP4K3, MAP4K4, MAP4K5, ZAK and v-akt murine thymoma viral oncogene homolog 1, AKT1, are among those expressed in significantly lower abundance in the highly metastasizing canine osteosarcoma cell line indicating changes in cell signaling. Chapter 5 describes the development and application of a multiple protease protocol (Trypsin, LysC, AspN, Chymotrypsin and GluC) for improving the number of phosphosite identifications in a large-scale phosphoproteomics studies. The method combines immobilized titanium ion affinity chromatography (Ti4+-IMAC) with a data-dependent, decision tree-based data acquisition technique utilizing two complementary fragmentation methods, namely collision induced dissociation (CID) and electron transfer dissociation. The multiple protease protocol was applied to human leukemic T cell lymphoblasts (Jurkat E6.1) and resulted in the detection of >11,000 unique phosphosites, the most comprehensive identification among methods that use similar phosphopeptide enrichment approach.

Download or read book Quantitative Methods in Proteomics written by Katrin Marcus and published by Humana Press. This book was released on 2012-06-06 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

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.

Download or read book Proteomics written by Tsz Kwong Man and published by BoD – Books on Demand. This book was released on 2012-02-10 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biomedical research has entered a new era of characterizing a disease or a protein on a global scale. In the post-genomic era, Proteomics now plays an increasingly important role in dissecting molecular functions of proteins and discovering biomarkers in human diseases. Mass spectrometry, two-dimensional gel electrophoresis, and high-density antibody and protein arrays are some of the most commonly used methods in the Proteomics field. This book covers four important and diverse areas of current proteomic research: Proteomic Discovery of Disease Biomarkers, Proteomic Analysis of Protein Functions, Proteomic Approaches to Dissecting Disease Processes, and Organelles and Secretome Proteomics. We believe that clinicians, students and laboratory researchers who are interested in Proteomics and its applications in the biomedical field will find this book useful and enlightening. The use of proteomic methods in studying proteins in various human diseases has become an essential part of biomedical research.

Download or read book Quantitative Proteome Analysis written by Kazuhiro Imai and published by CRC Press. This book was released on 2013-08-05 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Modern Proteomics Sample Preparation Analysis and Practical Applications written by Hamid Mirzaei and published by Springer. This book was released on 2016-12-14 with total page 525 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume serves as a proteomics reference manual, describing experimental design and execution. The book also shows a large number of examples as to what can be achieved using proteomics techniques. As a relatively young area of scientific research, the breadth and depth of the current state of the art in proteomics might not be obvious to all potential users. There are various books and review articles that cover certain aspects of proteomics but they often lack technical details. Subject specific literature also lacks the broad overviews that are needed to design an experiment in which all steps are compatible and coherent. The objective of this book was to create a proteomics manual to provide scientists who are not experts in the field with an overview of: 1. The types of samples can be analyzed by mass spectrometry for proteomics analysis. 2. Ways to convert biological or ecological samples to analytes ready for mass spectral analysis. 3. Ways to reduce the complexity of the proteome to achieve better coverage of the constituent proteins. 4. How various mass spectrometers work and different ways they can be used for proteomics analysis 5. The various platforms that are available for proteomics data analysis 6. The various applications of proteomics technologies in biological and medical sciences This book should appeal to anyone with an interest in proteomics technologies, proteomics related bioinformatics and proteomics data generation and interpretation. With the broad setup and chapters written by experts in the field, there is information that is valuable for students as well as for researchers who are looking for a hands on introduction into the strengths, weaknesses and opportunities of proteomics.

Download or read book Advancing Quantitative Proteomics and Protein Post translational Modification Analyses by Multi dimensional Mass Spectrometric Approaches written by Zihui Li and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are important molecules that are involved in numerous critical biological processes. Consequently, understanding the functional roles and dysregulation of proteins constitutes a vital task in both basic and clinical research. However, it is very challenging to define the full complement of proteins due to their large degree of variations, especially considering that many proteins can undergo numerous post-translational modifications (PTMs) which dramatically affect protein conformations and functions. Recently, mass spectrometry (MS) has evolved as a powerful tool to characterize proteins and their PTMs benefiting from its high speed, sensitivity and the ability to monitor thousands of analytes simultaneously. This dissertation is devoted to the development and application of various MS-based strategies to facilitate the detection of proteins and their PTMs qualitatively and quantitatively. A portion of this dissertation describes the investigation of proteome-wide alterations with the development and maturation of human pancreas using custom-developed isobaric tags. This study focuses on the extracellular matrix proteins and provides information on the localization changes of selected proteins in islet or acinar compartments as well. The normal baseline data across the lifespan of human pancreas will become a valuable resource and benefit future studies into the pancreatic pathologies. Switching gear to protein PTMs, this dissertation documents the design and development of a novel biotin thiol tag to greatly improve the in-depth profiling of two important PTMs, citrullination and homocitrullination, from complex biological samples. The utility of the approach is demonstrated by providing the first tissue-specific citrullination and homocitrullination atlas in mice. The first high-throughput quantitative analysis pipeline of protein citrullination is subsequently developed by the integration with isobaric labeling strategy. We also further improve the protein citrullination detection by using a combination of various digestion and fragmentation techniques. Citrullination alteration during the progression of Alzheimer's disease is further explored using human cerebrospinal fluid to shed light on the disease pathogenesis. This dissertation also highlights the application of a novel sub-atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry platform for the in situ imaging of N-glycans. Spatial distribution of N-glycans in ovarian cancer tissue section may indicate potential association of this modification with tumor progression. Collectively, we expect the biological insights and technological advancements presented in this work will lead to improved understanding of microenvironment in both healthy and disease conditions, and the new knowledge gained from these studies will inspire and benefit future research effort in related fields.

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.

Download or read book Mass Spectrometry Data Analysis in Proteomics written by Rune Matthiesen and published by Humana Press. This book was released on 2013-05-28 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably. Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics.