Download or read book Mass Spectrometry Applications for Comparative Proteomics and Peptidomic Discovery written by and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this thesis, multiple biological samples from various diseases models or treatments are investigated using shotgun proteomics and improved methods are developed to enable extended characterization and detection of neuropeptides. In general, this thesis aims to expand upon the rapidly evolving field of mass spectrometry (MS)-based proteomics and peptidomics by primarily enhancing small scale sample analysis. A review of the current status and progress in the field of biomarker discovery in peptidomics and proteomics is presented. To this rapidly expanding body of literature, our critical review offers new insights into MS-based biomarker studies investigating numerous biological samples, methods for post-translational modifications, quantitative proteomics, and biomarker validation. Methods are developed and presented, including immunodepletion for small volume cerebrospinal fluid (CSF) samples, for comparison of the CSF proteomes between an Alexander disease transgenic mouse model with overexpression of the glial fibrillary acidic protein and a control animal. This thesis also covers the application of the small scale immunodepletion of CSF for comparative proteomic analysis of a novel rat adapted scrapie (RAS) model for prion disease and compares the RAS CSF proteome to control rat CSF using MS. Large scale phosphoproteomics of starved vs. glucose fed yeast is presented to better understand the phosphoproteome changes that occur during glucose feeding. Method development for neuropeptide analysis is expanded upon using electron transfer dissociation (ETD) fragmentation to successfully sequence, for the first time, the crustacean hyperglycemic hormone precursor-related peptide (CPRP) from the blue crab Callinectes sapidus. In addition, a method for ETD sequencing of sulfonated neuropeptides using a magnesium salt adduct in an ion trap mass spectrometer is reported. This thesis also reports on a method for sub-ìg peptide isolation when using a molecular weight cut-off filtration device to improve sample recovery by over 2 orders of magnitude. All the protocols used throughout the work are provided in an easy to use step-by-step format in the Appendix. Collectively, this body of work extends the capabilities of mass spectrometry as a bioanalytical tool for shotgun proteomics and expands upon methods for neuropeptide discovery and analysis.
Download or read book Peptidomics written by Mikhail Soloviev and published by John Wiley & Sons. This book was released on 2007-12-21 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: The definitive guide to peptidomics- a hands-on lab reference The first truly comprehensive book about peptidomics for protein and peptide analysis, this reference provides a detailed description of the hows and whys of peptidomics and how the techniques have evolved. With chapters contributed by leading experts, it covers naturally occurring peptides, peptidomics methods and new developments, and the peptidomics approach to biomarker discovery. Explaining both the principles and the applications, Peptidomics: Methods and Applications: * Features examples of applications in diverse fields, including pharmaceutical science, toxicity biomarkers, and neuroscience * Details the successful peptidomic analyses of biological material ranging from plants to mammals * Describes a cross section of analytical techniques, including traditional methodologies, emerging trends, and new techniques for high throughput approaches An enlightening reference for experienced professionals, this book is sufficiently detailed to serve as a step-by-step guide for beginning researchers and an excellent resource for students taking biotechnology and proteomics courses. It is an invaluable reference for protein chemists and biochemists, professionals and researchers in drug and biopharmaceutical development, analytical and bioanalytical chemists, toxicologists, and others.
Download or read book Protein and Peptide Mass Spectrometry in Drug Discovery written by Michael L. Gross and published by John Wiley & Sons. This book was released on 2011-09-26 with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book that highlights mass spectrometry and its application in characterizing proteins and peptides in drug discovery An instrumental analytical method for quantifying the mass and characterization of various samples from small molecules to large proteins, mass spectrometry (MS) has become one of the most widely used techniques for studying proteins and peptides over the last decade. Bringing together the work of experts in academia and industry, Protein and Peptide Mass Spectrometry in Drug Discovery highlights current analytical approaches, industry practices, and modern strategies for the characterization of both peptides and proteins in drug discovery. Illustrating the critical role MS technology plays in characterizing target proteins and protein products, the methods used, ion mobility, and the use of microwave radiation to speed proteolysis, the book also covers important emerging applications for neuroproteomics and antigenic peptides. Placing an emphasis on the pharmaceutical industry, the book stresses practice and applications, presenting real-world examples covering the most recent advances in mass spectrometry, and providing an invaluable resource for pharmaceutical scientists in industry and academia, analytical and bioanalytical chemists, and researchers in protein science and proteomics.
Download or read book Proteomics and Peptidomics written by Gyorgy Marko-Varga and published by Elsevier. This book was released on 2005-12-23 with total page 663 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics and peptidomics is the detailed understanding of the role that proteins and peptides play in health and disease and is a necessary compliment to genetic analysis. The functional expression analysis of both proteins and peptides plays a central role in modern drug discovery as well as drug development, and is also a key research area in systems biology. Proteomics and Peptidomics captures the width as well as the depth within the area and exemplifies the variety as well as the traditional basis of analytical chemistry that is needed in order to move forward in expression analysis studies. As a fast emerging field, it gives and overview of parts within the field combined with highly specialized and dedicated topics that are intended to compliment each other.
Download or read book Peptidomics written by Michael Schrader and published by Humana. This book was released on 2019-06-04 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume describes protocols for basic state-of-the-art approaches in the field of peptidomics. Most of these approaches are independent of the instruments used for analysis and can easily be adapted for equipment that is available in a typical proteomics facility. Chapters detail many of the basic techniques used to detect and identify peptides, methods for the relative quantitation of peptides between samples using isotopic labels or label-free approaches, and biological species as well as sample types. Written in the highly successful format of the Methods in Molecular Biology series, each chapter includes an introduction to the topic, a list of the necessary materials and reagents, reproducible step-by-step laboratory protocols, and tips on troubleshooting common problems and avoiding pitfalls. Authoritative and practical, Peptidomics: Methods and Strategies provides useful guidance for studies in the rapidly growing field of peptidomics.
Download or read book Advancing Qualitative and Quantitative Proteomics peptidomics Via Development of Novel Mass Spectrometry based Approaches written by Qing Yu and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Liquid chromatography mass spectrometry (LC-MS) has evolved as a powerful tool in protein and peptide identification and quantitation. It has the capability to monitor thousands of proteins and peptides simultaneously and therefore is a critical component in the study of underlying biological mechanisms and the discovery of novel therapeutic targets. This dissertation is devoted to the development and application of novel LC-MS based techniques to characterize proteomics and peptidomics qualitatively and quantitatively by incorporating various sample preparation strategies, novel MS methods and isobaric labeling technology. A portion of this dissertation describes the design and evaluation of several dimethylated amino acid tags and their potentials to be used as isobaric labeling reagents for protein and peptide quantitation. Their utilities are further demonstrated through their application in the study of global proteomic changes in models of restenosis. Although isobaric tags are originally designed for higher-energy collisional dissociation (HCD), we expand their use by enabling them to be coupled with electron-transfer/higher-energy collision dissociation (EThcD) fragmentation. The benefits of using such strategy in quantitative proteomics, especially phosphorylation studies, are recounted in this dissertation. Quantitative strategies presented in this dissertation are complemented by advances in MS-based protein and endogenous peptide sequencing methodologies. We established a workflow to sequence intact glycopeptides, enabling detailed investigation of complex protein glycosylation and its microheterogeneity. The application of this improved workflow revealed a hyperglycosylation trend from day 0 to day 7 post angioplasty along the progression of restenosis. Similarly, by employing a further modified strategy, this dissertation documented the discovery of O-linked glycosylation on endogenous signaling peptides, specifically insulin and its related peptide hormones. The significance of such discovery can be critical toward diabetes research and treatment. Meanwhile, this dissertation also describes the strategy to characterize large neuropeptides in a species with no genome information, which can be greatly useful for future neuropeptide research. Furthermore, we employ ion mobility MS (IM-MS) to study peptide structures and conformations, leading to discovery of D-amino acid containing peptides based on subtle changes in gas-phase conformations despite identical mass-to-charge ratio. The IM-MS strategy enables the study of this unique isobaric post-translational modification (PTM) in neuropeptides occurring via amino acid isomerization. Overall, this dissertation research not only improves upon isobaric labeling technique by exploring novel chemical tags and new fragmentation methods, but also presents a useful platform to enable in-depth investigation on complex PTMs and subtle conformational differences. Collectively, we expect that the technology advancements presented in this work will enable broad applications in various biological systems and lead to improved understanding of underlying molecular mechanisms.
Download or read book Advancements of Mass Spectrometry in Biomedical Research written by Alisa G. Woods and published by Springer. This book was released on 2014-06-20 with total page 601 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the use of mass spectrometry for biomedical applications. Chapters focus on specific therapeutic areas such as oncology, infectious disease and psychiatry. Additional chapters focus on methodology as well as new technologies and instrumentation. This volume provides readers with a comprehensive and informative manual that will allow them to appreciate mass spectrometry and proteomic research but also to initiate and improve their own work. Thus the book acts as a technical guide but also a conceptual guide to the newest information in this exciting field. Mass spectrometry is the central tool used in proteomic research today and is rapidly becoming indispensable to the biomedical scientist. With the completion of the human genome project and the genomic revolution, the proteomic revolution has followed closely behind. Understanding the human proteome has become critical to basic and clinical biomedical research and holds the promise of providing comprehensive understanding of human physiological processes. In addition, proteomics and mass spectrometry are bringing unprecedented biomarker discovery and are helping to personalize medicine.
Download or read book Comparative Proteomic Profiling and Biomarker Discovery in Complex Biological Samples by Mass Spectrometry written by and published by . This book was released on 2012 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in mass spectrometry (MS) technology have made MS-based proteomics a promising tool for protein profiling and biomarker discovery. However, MS analyses of biological samples are challenging due to their vast complexity and large dynamic range. Because disease identifying biomarkers are likely low abundance proteins, it is imperative to remove high abundance proteins or apply enrichment techniques during sample preparation to detect and improve coverage of low abundance proteins. In addition, the complexity of the digested biological samples can be reduced by applying multiple orthogonal separations prior to LC-MS/MS such as multidimensional protein identification technology (MudPIT). In this dissertation, the major objectives include the following: (1) method development of sample preparation and chromatographic separation for MS-based quantitative proteomics, and (2) their applications in large-scale protein characterization in complex biological samples for differential expression analysis and biomarker discovery will be discussed. First, MudPIT combined with ESI-MS/MS was optimized for global proteome profiling in naïve and interleukin-2 (IL-2)-activated natural killer cells to identify IL-2 regulated proteins that elucidate new pathways associated with IL-2 signaling. A similar strategy was also applied to the comparative secretome analysis in rat vascular smooth muscle cells (VSMCs) stimulated by transforming growth factor-beta; (TGF-beta), which led to the identification of secreted proteins that may be associated with TGF-beta; signaling in VSMCs. In a third project, lectin affinity chromatography (LAC) was utilized in sample preparation of mouse plasma affected by prion disease to specifically enrich glycoproteins that may prove to be important biomarkers for prion diseases. The combination of LAC and MudPIT significantly reduced sample complexity and led to the discovery of a panel of potential biomarkers including the validation of serum amyloid P-component (SAP). Furthermore, PNGase F digestion analysis confirmed that the glycosylated form of SAP could be used as a potential diagnostic biomarker for prion diseases. Collectively, the work included in this thesis extends the capability of mass spectrometry as a powerful analytical tool for large-scale proteomic analysis in complex biological samples to identify disease biomarkers or biomolecules involved in critical cellular processes.
Download or read book Mass Spectrometry of Proteins written by Caroline A. Evans and published by . This book was released on 2019 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Application of Label free Mass Spectrometry based Proteomics to Biomarker Discovery written by Susan E. Slade and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Proteomics for Food Authentication written by Leo M.L. Nollet and published by CRC Press. This book was released on 2020-05-07 with total page 193 pages. Available in PDF, EPUB and Kindle. Book excerpt: Consumers have the right to know what is in the food they are eating, and accordingly, a number of global food regulations require that the provenance of the food can be guaranteed from farm to fork. Many different instrumental techniques have been proposed for food authentication. Although traditional methods are still being used, new approaches such as genomics, proteomics, and metabolomics are helping to complement existing methodologies for verifying the claims made about certain food products. During the last decade, proteomics (the largescale analysis of proteins in a particular biological system at a particular time) has been applied to different research areas within food technology. Since proteins can be used as markers for many properties of a food, even indicating processes to which the food has been subjected, they can provide further evidence of the foods labeling claim. Proteomics for Food Authentication, a volume in the Food Analysis and Properties Series, is a comprehensive and updated overview of the applications, drawbacks, advantages, and challenges of proteomics for food authentication. Features: Provides a comprehensive and critical overview of the application of proteomics in food Helps food scientists determine the authenticity of several food products Provides applied techniques for both laboratory and industrial environments Describes workflows, technologies, and tools that are being assessed in proteomics-related studies Workflows, technologies, and tools that are being assessed in proteomics-related studies are described, followed by a review of the specific applications regarding food authenticity and, now and then, food quality. The book will provide a comprehensive and critical overview of the application of proteomics approaches to determine the authenticity of several food products updating the performances and current limitations of the applied techniques in both laboratory and industrial environments. As such it is well suited to food scientist, chemical engineers, food engineers, research labs, universities, governments, related food industries. Also available in the Food Analysis and Properties Series: Food Aroma Evolution: During Food Processing, Cooking, and Aging, edited by Matteo Bordiga and Leo M.L. Nollet (ISBN: 9781138338241) Ambient Mass Spectroscopy Techniques in Food and the Environment, edited by Leo M.L. Nollet and Basil K. Munjanja (ISBN: 9781138505568) Hyperspectral Imaging Analysis and Applications for Food Quality, edited by N.C. Basantia, Leo M.L. Nollet, and Mohammed Kamruzzaman (ISBN: 9781138630796) For a complete list of books in this series, please visit our website at: www.crcpress.com/Food-Analysis--Properties/book-series/CRCFOODANPRO
Download or read book Separation Techniques Applied to Omics Sciences written by Ana Valéria Colnaghi Simionato and published by Springer Nature. This book was released on 2021-10-09 with total page 277 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers liquid chromatography, gas chromatography and capillary electrophoresis, the three main separation techniques lately available, applied to key omic sciences, such as genomics, proteomics, metabolomics and foodomics. The fundamentals of each technique are not covered herein. Instead, the recent advances in such techniques are presented focusing on the application to omics analyses and unique aspects in each case. This volume intends to offer wide ranging options available to researchers on omics sciences, and how to integrate them in order to achieve the comprehension of a biological system as a whole. Omic sciences have been of ultimate importance to comprehend the complex biochemical reactions and related events that occurs upon a biological system. The classical central dogma of molecular biology, which states that genetic information flows unidirectionally from DNA to RNA and then to proteins, has been gradually replaced by the systems biology approach. This book presents a multidisciplinary approach that explains the biological system as a whole, where the entire organism is influenced by a variety of internal events as well as by the environment, showing that each level of the biological information flux may influence the previous or the subsequent one.
Download or read book Foodomics written by Alejandro Cifuentes and published by John Wiley & Sons. This book was released on 2013-03-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides the latest "-omics" tools to advance the study of food and nutrition The rapidly emerging field of foodomics examines food and nutrition by applying advanced "-omics" technologies in order to improve people's health, well-being, and knowledge. Using tools from genomics, transcriptomics, epigenomics, proteomics, and metabolomics, foodomics offers researchers new analytical approaches to solve a myriad of current challenges in food and nutrition science. This book presents the fundamentals of foodomics, exploring the use of advanced mass spectrometry techniques in food science and nutrition in the post-genomic era. The first chapter of the book offers an overview of foodomics principles and applications. Next, the book covers: Modern instruments and methods of proteomics, including the study and characterization of food quality, antioxidant food supplements, and food allergens Advanced mass spectrometry-based methods to study transgenic foods and the microbial metabolome Mass spectrometry-based metabolomics in nutrition and health research Foodomics' impact on our current understanding of micronutrients (phenolic compounds and folates), optimal nutrition, and personalized nutrition and diet related diseases Principles and practices of lipidomics and green foodomics Use of chemometrics in mass spectrometry and foodomics The final chapter of Foodomics explores the potential of systems biology approaches in food and nutrition research. All the chapters conclude with references to the primary literature, enabling readers to explore individual topics in greater depth. With contributions from a team of leading pioneers in foodomics, this book enables students and professionals in food science and nutrition to take advantage of the latest tools to advance their research and open up new areas of food and nutrition investigation.
Download or read book Neuropeptides and Other Bioactive Peptides written by Lloyd D. Fricker and published by Morgan & Claypool Publishers. This book was released on 2012 with total page 123 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neuropeptides and peptide hormones represent the largest class of chemical messengers that transmit information from one cell to another. In this review, several decades of research on peptides in cell-cell signaling are summarized, with a focus on neuropeptide discovery, biosynthesis, and function. In addition to covering the well-studied aspects of neuropeptides, emerging concepts are discussed, including classical versus non-classical neuropeptides and direct versus indirect neuropeptides. Other potential functions for peptides in intercellular and intracellular signaling are also discussed. Table of Contents: Overview of Neuropeptides / Neuropeptide Discovery / Neuropeptide Biosynthesis / Neuropeptides After Secretion: Receptors and Peptidases / Representative Neuropeptides / Concluding Remarks and Future Directions / References / Author Biography
Download or read book Food Exploitation By Social Insects written by Stefan Jarau and published by CRC Press. This book was released on 2009-05-21 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Omnipresent in virtually all terrestrial ecosystems and of undisputed ecological and economical importance, the study of social insects is an area that continues to attract a vast number of researchers. As a consequence, a huge amount of information about their biology and ecology has accumulated. Distilling this scattered information into a highly
Download or read book Activity Based Protein Profiling written by Benjamin F. Cravatt and published by Springer. This book was released on 2019-01-25 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a collection of contemporary perspectives on using activity-based protein profiling (ABPP) for biological discoveries in protein science, microbiology, and immunology. A common theme throughout is the special utility of ABPP to interrogate protein function and small-molecule interactions on a global scale in native biological systems. Each chapter showcases distinct advantages of ABPP applied to diverse protein classes and biological systems. As such, the book offers readers valuable insights into the basic principles of ABPP technology and how to apply this approach to biological questions ranging from the study of post-translational modifications to targeting bacterial effectors in host-pathogen interactions.
Download or read book Proteome Informatics written by Conrad Bessant and published by Royal Society of Chemistry. This book was released on 2016-11-15 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of proteomics has developed rapidly over the past decade nurturing the need for a detailed introduction to the various informatics topics that underpin the main liquid chromatography tandem mass spectrometry (LC-MS/MS) protocols used for protein identification and quantitation. Proteins are a key component of any biological system, and monitoring proteins using LC-MS/MS proteomics is becoming commonplace in a wide range of biological research areas. However, many researchers treat proteomics software tools as a black box, drawing conclusions from the output of such tools without considering the nuances and limitations of the algorithms on which such software is based. This book seeks to address this situation by bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, so that users of proteomics data can be confident that they are using appropriate tools in suitable ways.
