Download or read book Neuropeptidomics MS base Peptide Identification and Quantitation Study written by Ping Yin and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Neuropeptidomics refers to a global characterization approach for the investigation of neuropeptides, often under specific physiological conditions. Neuropeptides comprise a complex set of cell-to-cell signaling molecules that are important in regulatory functions and behavior in the nervous system. Neuropeptide production typically involves endoproteolytic prohormone cleavage, exoproteolytic cleavage, and post-translational modifications by a variety of enzymes. Neuropeptides are packaged into and eventually released from the large dense-core vesicles in a regulated secretory pathway. Neuropeptidomics is inherently challenging because neuropeptides are spatially, temporally and chemically heterogeneous in the brain. In addition, the unconventional peptide precursor cleavages and various post-translational modifications require the unbiased measurements of actual peptide forms. Mass spectrometry (MS), coupled with optimized liquid chromatography separation and aided by appropriate sample preparation, has been successfully applied for peptide identification and quantitation. Neuropeptide production regulated by DIMM-dependent genetic mechanism and post-translational processing through alpha-amidation has been studied with different MS-based approaches such as matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and electrospray ionization ion-trap (ESI-IT) MS. DIMM, a transcription factor in Drosophila, appears able to make non-peptidergic cells into peptidergic neurons. Qualitative MS approaches allowed us to observe the fully processed ectopic peptide MII in Drosophila non-peptidergic cells only when DIMM was present. Quantitative MS approaches, together with molecular biological methods, revealed DIMM enabled this complete and efficient ectopic peptide processing through regulating gene CG13248. In addition, an important post-translational modification, peptide alpha-amidation, was studied with mice of different genotypes on different copper diets. The results on the peptide level changes of mature peptides and their immature intermediate forms facilitate our understanding on peptide amidation reaction and its dedicated enzyme peptidylglycine alpha-amidating monooxygenase (PAM). Neurons and glia are two main types of cells in the central nervous system. Analogous to neuropeptidome, the knowledge of the gliopeptidome would aid our understanding of the interaction between glia and neurons. Therefore, the peptides in and regulatedly released from glia were examined. Peptides derived from proteins or putatively from neuropeptide precursors were identified with liquid chromatography coupled to mass spectrometry (LC-MS). Future studies would focus on the confirmation of the putatively identified peptides and the functions of identified peptides in glia. This dissertation demonstrates MS-based approaches are useful tools for probing peptides qualitatively and quantitatively, which would greatly expand our understanding of cell-to-cell communication in the nervous system.
Download or read book Discovery and Quantification of Crustacean Neuropeptides Using Mass Spectrometry and Informatics Approaches written by Nhu Vu and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of endogenous peptides is important for discovering critical elements involved in many physiological processes and disorders. Neuropeptides are endogenous peptide hormones that regulate these processes by binding to receptors to initiate cellular signaling pathways. Discovery of neuropeptide function is an increasingly popular avenue for disease therapeutics research, resulting in increased need for improved neuropeptide characterization methods. Although mass spectrometry (MS) is well-suited for neuropeptide analysis due to its high sensitivity and capacity for untargeted, global neuropeptide measurements, there are still technical challenges that must be overcome. For example, neuropeptide sequences within a peptide family are highly homologous and therefore must be analyzed in their intact form to obtain high sequence coverage for confident identification and often require high resolution instrumentation. This becomes more challenging as sequence length and post-translational modification complexity increases. In this thesis, I will discuss my efforts in improving MS-based neuropeptidomic workflows, specifically in relation to "top-down" protein and peptide characterization, while highlighting improvements in identification and quantification of peptides through optimized fragmentation and cysteine reactive labeling. I will also discuss my contributions to our group's novel software, HyPep, enabling utility for confident neuropeptide identification. Altogether, these methods have contributed to increased neuropeptide coverage and can be translated to the analysis of other peptide classes.This thesis begins with two reviews of recent developments in MS-based analysis of neuropeptides. Each review outlines examples of how advancements in MS sample preparation, MS acquisition, data analysis, and technology has increased our understanding of neuropeptides, and provides insight on promising directions for further development within each section. My research contributions in Professor Lingjun Li's research group started by applying peptidomics workflows to quantify changes in neuropeptide expression due to hypoxia stress in a crustacean animal model, C. sapidus. Using the same animal model, we also increased the number of detectable neuropeptides using matrix-assisted laser desorption/ionization (MALDI)-MS imaging by incorporating novel tissue wash steps during sample preparation. Over 100 putative peptidomic biomarkers for different levels of hypoxia severity and duration were discovered within multiple tissue types. Four neuropeptide biomarkers were examined for functional activity and two neuropeptides were discovered to increase cardiac output ex vivo, including the first-ever reported function for a crustacean hyperglycemic hormone precursor-related peptide (CPRP). Since CPRP (3.5 kDa) is co-released with crustacean hyperglycemic hormone (CHH) neuropeptide (8.5 kDa), an important neuropeptide that regulates glucose metabolism, we did not detect CHH in these hypoxia studies because its larger size prevented confident detection using typical neuropeptidomic MS workflow and data acquisition methods. Previous members of our research group have developed MS methods to sequence CHH, but limitations of those methods included requiring multiple MS instruments or reliance on targeted MS strategies in which information of potential novel neuropeptides is lost. I built upon those MS acquisition and data analysis methods and was able to sequence novel CHH isoforms and proteoforms, without assistance from genomic or transcriptomic-based sequence prediction, using a Thermo Orbitrap Fusion Lumos instrument. Additionally, I developed novel sample preparation methods to reduce the disulfide bonds and alkylate all six cysteine residues on CHH at high efficiency (83-89% labeling efficiency). While developing methods for CHH are beneficial for analyzing mid-size (8-10 kDa) peptides, I sought to also advance general neuropeptidomics data analysis pipeline. A novel concept for neuropeptide identification software, called HyPep, was created 10 years ago but was not finished and could not be used. To make the software usable, I incorporated features typically used in peptide-spectrum matching (PSM)-based algorithms in proteomics software, such as a false discovery rate. I optimized the software parameters which resulted in HyPep outperforming an analogous commercial software in identifying neuropeptides from four crustacean neuronal tissue types. Collectively, this dissertation is devoted to advancing sample preparation, data acquisition, and data analysis strategies for neuropeptidomics, and these methods are also potentially translatable to analyze other classes of endogenous peptides.
Download or read book Probing Neuropeptidomics by Mass Spectrometry written by and published by . This book was released on 2012 with total page 548 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this thesis, an array of biological mass spectrometry (MS) based methods were developed and employed to enable the identification and functional analysis of neuropeptides in the crustacean nervous system. Neuropeptides encompass the largest and most diverse group of signaling molecules in the nervous system. They are necessary for the initiation and regulation of numerous physiological processes such as feeding, reproduction and development. However, the discovery and identification of these important signaling molecules presents unique challenges due to the vast complexity and minute quantities of endogenously expressed peptides. Further functional analysis of neuropeptides needs to be conducted for a comprehensive neuropeptidomic study. Using the decapod crustacean nervous system and associated neuroendocrine organs as experiment model, this dissertation research focuses on the development of an integrated analytical platform for large-scale identification and discovery of neuropeptides, as well as investigation of the functional roles of neuropeptides. The work presented here contributes insight into neuropeptidome of a commercially and scientifically important crustacean species, blue crab /italicCallinectes sapidus/italic and the possible functionality of certain peptides. A multifaceted mass spectrometry approach combining complementary sample preparation techniques, advanced separation strategies, alternative fragmentation methods, mass spectral imaging (MSI) and stable isotopic labeling was used for large-scale identification and to provide comprehensive information on peptide expression level changes under different physiological states. Several new analytical methodologies and tools have been developed to enable enhanced neuropeptidome coverage and improved /italicde novo/italic sequencing. A two dimensional liquid chromatography (2D-LC) method coupling reversed-phase liquid chromatography (RPLC) with nano-LC-ESI-Q-TOF MS/MS was used for neuronal tissue extract analysis and greatly improved the neuropeptidome coverage. A homemade capillary isoelectric focusing (cIEF) system was used for separation of the most acidic neuropeptide family Orcokinins in the sinus gland (SG). Additionally, electron transfer dissociation (ETD) was employed for the identification and sequencing of intact crustacean hyperglycemic hormone precursor related peptides (CPRPs), a group of multiply charged peptides in the SG. More than 150 neuropeptides including over 40 novel ones were identified in blue crab's nervous system. Furthermore, a comparative peptidomic study utilized mass spectral imaging (MSI), stable isotopic labeling and electrophysiological study was developed to provide comprehensive information about peptide expression level changes after food intake. Moreover, a MS-based platform was developed to study the differential degradation of neuropeptides by extracellular peptidases via monitoring degradation rate and degradation products. Collectively, this body of work extends the capability of mass spectrometry as a bioanalytical tool for neuropeptide analysis and advances the basic understanding of neuronal signaling.
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 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 Brain Peptides written by Dorothy T. Krieger and published by Wiley-Interscience. This book was released on 1983-11-14 with total page 1054 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first major comprehensive overview of the anatomical, physiological, evolutionary, and embryological aspects of brain peptides, focusing on peptides described in the past decade. Examines the role of peptides in affecting major homeostatic systems. Presents the methodologies applicable to the study of brain peptides. Summarizes current knowledge of individual peptides.
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 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 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 Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2006-06-12 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Fundamentals and Applications of Fourier Transform Mass Spectrometry written by Philippe Schmitt-Kopplin and published by Elsevier. This book was released on 2019-08-11 with total page 778 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fundamentals and Applications of Fourier Transform Mass Spectrometry is the first book to delve into the underlying principles on the topic and their linkage to industrial applications. Drs. Schmitt-Kopplin and Kanawati have brought together a team of leading experts in their respective fields to present this technique from many different perspectives, describing, at length, the pros and cons of FT-ICR and Orbitrap. Numerous examples help researchers decide which instruments to use for their particular scientific problem and which data analysis methods should be applied to get the most out of their data. Covers FT-ICR-MS and Orbitrap’s fundamentals, enhancing researcher knowledge Includes details on ion sources, data processing, chemical analysis and imaging Provides examples across the wide spectrum of applications, including omics, environmental, chemical, pharmaceutical and food analysis
Download or read book Neuropeptide Systems as Targets for Parasite and Pest Control written by Timothy G. Geary and published by Springer Science & Business Media. This book was released on 2011-01-13 with total page 246 pages. Available in PDF, EPUB and Kindle. Book excerpt: The need to continually discover new agents for the control or treatment of invertebrate pests and pathogens is undeniable. Agriculture, both animal and plant, succeeds only to the extent that arthropod and helminth consumers, vectors and pathogens can be kept at bay. Humans and their companion animals are also plagued by invertebrate parasites. The deployment of chemical agents for these purposes inevitably elicits the selection of resistant populations of the targets of control, necessitating a regular introduction of new kinds of molecules. Experience in other areas of chemotherapy has shown that a thorough understanding of the biology of disease is an essential platform upon which to build a discovery program. Unfortunately, investment of research resources into understanding the basic physiology of invertebrates as a strategy to illuminate new molecular targets for pesticide and parasiticide discovery has been scarce, and the pace of introduction of new molecules for these indications has been slowed as a result. An exciting and so far unexploited area to explore in this regard is invertebrate neuropeptide physiology. This book was assembled to focus attention on this promising field by compiling a comprehensive review of recent research on neuropeptides in arthropods and helminths, with contributions from many of the leading laboratories working on these systems.
Download or read book Triatominae The Biology of Chagas Disease Vectors written by Alessandra Guarneri and published by Springer Nature. This book was released on 2021-07-06 with total page 642 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book aims to present updated knowledge on various aspects of the natural history, biology, and impact of triatomines to all interested readers. Each chapter will be written by authorities in the respective field, covering topics such as behavior, neurophysiology, immunology, ecology, and evolution. The contents will consider scientific, as well as innovative perspectives, on the problems related to the role of triatomine bugs as parasite vectors affecting millions in the Latin American region.
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 Endocrinology and Metabolism written by Philip Felig and published by McGraw-Hill Companies. This book was released on 1981 with total page 1408 pages. Available in PDF, EPUB and Kindle. Book excerpt: * Written by leading clinicians with greater emphasis on clinical practice, rather than basic science
Download or read book Systems Neuroscience written by Albert Cheung-Hoi Yu and published by Springer. This book was released on 2018-10-17 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: This edition of Advances in Neurobiology brings together experts in the emerging field of Systems Neuroscience to present an overview of this area of research. Topics covered include: how different neural circuits analyze sensory information, form perceptions of the external world, make decisions, and execute movements; how nerve cells behave when connected together to form neural networks; the relationship between molecular and cellular approaches to understanding brain structure and function; the study of high-level mental functions; and studying brain pathologies and diseases with Systems Neuroscience. A hierarchy of biological complexity arises from the genome, transcriptome, proteome, organelles, cells, synapses, circuits, brain regions, the whole brain, and behaviour. The best way to study the brain, the most complex organ in the body composed of 100 billion cells with trillions of interconnections, is with a Systems Biology approach. Systems biology is an inter-disciplinary field that focuses on complex interactions within biological systems to reveal 'emergent properties' - properties of cells and groups of cells functioning as a system whose actual and theoretical description is only possible using Systems Biology techniques.
Download or read book The Crustacean Nervous System written by Konrad Wiese and published by Springer Science & Business Media. This book was released on 2002 with total page 652 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique selection of reviews summarizes current knowledge in all major fields of crustacean neurobiology and all levels of their CNS organization, using lobster and crayfish. It not only imparts theoretical knowledge but also describes all available contemporary and advanced techniques, such as patch clamp recordings, microelectrode techniques, immunocytochemistry, and all methods of molecular genetics to identify cellular pathways of protein synthesis and peptidergic control. In summary, it is a comprehensive account of the research achievements in one of the major nervous systems besides the mammalian CNS.
