Download or read book Sampling Strategies for Characterization of Neuropeptides Using Mass Spectrometry and Functional Implications Into Cell cell Signaling written by Adriana Bora and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In this dissertation, there are developed different analytical strategies to discover and characterize mammalian brain peptides using small amount of tissues. The magnocellular neurons of rat supraoptic nucleus in tissue and cell culture served as the main model to study neuropeptides, in addition to hippocampal neurons and mouse embryonic pituitaries. The neuropeptidomcis studies described here use different extraction methods on tissue or cell culture combined with mass spectrometry (MS) techniques, matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). These strategies lead to the identification of multiple peptides from the rat/mouse brain in tissue and cell cultures, including novel compounds One of the goals in this dissertation was to optimize sample preparations on samples isolated from well-defined brain regions for mass spectrometric analysis. Here, the neuropeptidomics study of the SON resulted in the identification of 85 peptides, including 20 unique peptides from known prohormones. This study includes mass spectrometric analysis even from individually isolated magnocellular neuroendocrine cells, where vasopressin and several other peptides are detected. At the same time, it was shown that the same approach could be applied to analyze peptides isolated from a similar hypothalamic region, the suprachiasmatic nucleus (SCN). Although there were some overlaps regarding the detection of the peptides in the two brain nuclei, different peptides were detected specific to each nucleus. Among other peptides, provasopressin fragments were specifically detected in the SON while angiotensin I, somatostatin-14, neurokinin B, galanin, and vasoactive-intestinal peptide (VIP) were detected in the SCN only. Lists of peptides were generated from both brain regions for comparison of the peptidome of SON and SCN nuclei. Moving from analysis of magnocellular neurons in tissue to cell culture, the direct peptidomics of the magnocellular and hippocampal neurons led to the detection of 10 peaks that were assigned to previously characterized peptides and 17 peaks that remain unassigned. Peptides from the vasopressin prohormone and secretogranin-2 are attributed to magnocellular neurons, whereas neurokinin A, peptide J, and neurokinin B are attributed to cultured hippocampal neurons. This approach enabled the elucidation of cell-specific prohormone processing and the discovery of cell-cell signaling peptides. The peptides with roles in the development of the pituitary were analyzed using transgenic mice. Hes1 KO is a genetically modified mouse that lives only e18.5 (embryonic days). Anterior pituitaries of Hes1 null mice exhibit hypoplasia due to increased cell death and reduced proliferation and in the intermediate lobe, the cells differentiate abnormally into somatotropes instead of melanotropes. These previous findings demonstrate that Hes1 has multiple roles in pituitary development, cell differentiation, and cell fate. AVP was detected in all samples. Interestingly, somatostatin [92-100] and provasopressin [151-168] were detected in the mutant but not in the wild type or heterozygous pituitaries while somatostatin-14 was detected only in the heterozygous pituitary. In addition, the putative peptide corresponding to m/z 1330.2 and POMC [205-222] are detected in the mutant and heterozygous pituitaries, but not in the wild type. These results indicate that Hes1 influences the processing of different prohormones having possible roles during development and opens new directions for further developmental studies. This research demonstrates the robust capabilities of MS, which ensures the unbiased direct analysis of peptides extracted from complex biological systems and allows addressing important questions to understand cell-cell signaling in the brain.
Download or read book Analysis of Neuropeptides by Liquid Chromatography and Mass Spectrometry written by D.M. Desiderio and published by Elsevier. This book was released on 2000-04-01 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: Analysis of Neuropeptides by Liquid Chromatography and Mass Spectrometry
Download or read book Methods in Neurotransmitter and Neuropeptide Research written by S.H. Parvez and published by Elsevier. This book was released on 2013-10-22 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: This two-part book provides the most advanced biochemical and histochemical analytical methods on neurotransmitters, neuromodulators, and neuropeptides described by international specialists. The biochemical methods include liquid chromatography/electrochemistry, liquid chromatography/fluorescence and chemiluminescence detection, gas chromatography or liquid chromatography with mass spectrometry, and immunoassays. Morphological and physiological methods are also described, including immunohistochemistry, in situ hybridization, in vivo microdialysis, electrophysiological analysis, microwave irradiation, electrophysiological analysis, micro-anatomical dissection, peptide sequence analysis, quantitative autoradiographic analysis, and isolated CNS preparations. The neurotransmitters and neuropeptides include catecholamines, indoleamines, histamine, polyamines, and various neuropeptides, and their related enzymes. The book is the most comprehensive, advanced and versatile volume on the biochemical, morphological and physiological analysis of neurotransmitters and neuropeptides.
Download or read book New Methods in Peptide Mapping for the Characterization of Proteins written by William S. Hancock and published by CRC Press. This book was released on 1995-10-23 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text is devoted to the characterization of recombinant DNA-derived proteins by peptide mapping. It describes new technological procedures including capillary electrophoresis, analysis of glycopeptides and the use of electrospray and matrix-assisted laser desorption mass spectrometry. The book presents practical procedures for preparing a protein sample, the enzyme digestion, choice of separation method and procedures for the structural analysis of the separated species. Many figures of peptide maps illustrate typical results. Tables of summary information about digestion, separation conditions, and analyses of important protein samples are also presented.
Download or read book Mass Spectrometry based Neuropeptidomic Study and Functional Discovery of Signaling Peptides written by Yang Liu and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neuropeptides are a group of signaling molecules with great diversity and significant functions in the regulation of physiological processes. The sequence identifications and stress-related studies are highly important in the systematic neuropeptidome characterization of a biological model. Crustaceans are one of the most commonly used animal models in neuropeptide research, providing a simple and well-characterized nervous system. Mass spectrometry (MS) has evolved as a prominent strategy in neuropeptide study, benefiting from its high resolution, high speed and high sensitivity. This dissertation is devoted to the development and application of MS-based techniques in multi-scale characterization of the crustacean neuropeptidome both qualitatively and quantitatively by incorporating various sample collection strategies, sample preparation protocols and MS methods. Collectively, the comprehensive investigation of neuropeptidome documented in this dissertation will lay a solid foundation for future studies of the functional roles of peptide hormones in the crustacean nervous system and the MS-based workflows introduced here will find widespread applications in the studies of signaling molecules utilized by various biological systems.
Download or read book Mass Spectrometry and Hyphenated Techniques in Neuropeptide Research written by Jerzy Silberring and published by John Wiley & Sons. This book was released on 2002-05-02 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first authoritative guide to the application of this vital analytical technique Mass spectrometry is a powerful analytical technique that is used to identify unknown compounds, to quantify known materials, and to elucidate the structural and chemical properties of molecules. In analyzing the effects of experimental drugs on the brain, it is the sole technique for identifying the presence and structure of neuropeptides-substances that indicate the effect of the drug. Mass Spectrometry and Hyphenated Techniques in Neuropeptide Research specifically explains how to apply the technology to this process. Because the book is written by mass spectrometry users, as opposed to mass spectrometrists, the focus remains on practical applications of the technique. The authors demonstrate how mass spectrometry works, how to apply the technique to research, which types of instrumentation should be used for particular requirements, and how to plan experiments. Readers will learn why mass spectrometry provides more outcome features than other techniques in neuropeptide analysis, including simultaneous detection, identification of substances present in mixtures, and sequence information even when the residues are modified, blocked, or unusual. Among the chapters in this comprehensive text are: * Sequencing of Peptides by Nanospray Mass Spectrometry * Laser-Machined Microdevices for Mass Spectrometry * Electron Capture Dissociation of Peptides * Synthesis of Combinatorial Peptide Libraries * Analysis of Tissues That Reflect Nervous System Disease Doctoral students, researchers, and industry professionals in pharmacology, chemistry, biochemistry/biotechnology, and medicine will find Mass Spectrometry and Hyphenated Techniques in Neuropeptide Research to be an indispensable starting point for understanding peptides, their function, and identification.
Download or read book Neuropeptide Protocols Methods in Molecular Biology written by G. Brent Irvine and published by . This book was released on 1997 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: Leading scientists offer an unprecedented suite of master protocols for analyzing neuropeptide structure and function using optimized classic methods and the latest state-of-the-art techniques. This comprehensive collection includes valuable techniques for extracting and purifying neuropeptides from biological sources, for their sequence determination by Edman degradation and PCR, and for the solid-phase synthesis and purification of peptides and peptide analogs. Also covered are physical techniques for the characterization of synthetic or natural peptides, methods for immunocytochemical sample preparation and visualization at both light and electron levels, and techniques for neuropeptide-receptor interaction. Chapters on molecular modeling, radioisotopic labeling, production of antisera, the measurement of efflux from brain to blood, and the assay and inhibition of neuropeptidases complete this indispensable collection of readily reproducible protocols.
Download or read book Characterization of Neuropeptides in Ascaris Suum Using Mass Spectrometry written by Joanne Y. Yew and published by . This book was released on 2003 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Neuropeptide Signaling in Crustaceans Probed by Mass Spectrometry written by and published by . This book was released on 2016 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neuropeptides are one of the most diverse classes of signaling molecules whose identities and functions are not yet fully understood. They have been implicated in the regulation of a wide range of physiological processes, including feeding-related and motivated behaviors, and also environmental adaptations. In this work, improved mass spectrometry-based analytical platforms were developed and applied to the crustacean systems to characterize signaling molecules. This dissertation begins with a review of mass spectrometry-based neuropeptide studies from both temporal- and spatial-domains. This review is then followed by several chapters detailing a few research projects related to the crustacean neuropeptidomic characterization and comparative analysis. The neuropeptidome of crayfish, Orconectes rusticus is characterized for the first time using mass spectrometry-based tools. In vivo microdialysis sampling technique offers the capability of direct sampling from extracellular space in a time-resolved manner. It is used to investigate the secreted neuropeptide and neurotransmitter content in Jonah crab, Cancer borealis, in this work. A new quantitation strategy using alternative mass spectrometry data acquisition approach is developed and applied for the first time to quantify neuropeptides. Coupling of this method with microdialysis enables the study of neuropeptide dynamics concurrent with different behaviors. Proof-of-principle experiments validating this approach have been carried out in Jonah crab, Cancer borealis to study feeding- and circadian rhythm-related neuropeptide changes using micoridialysis in a time-resolved manner. This permits a close correlation between behavioral and neurochemical changes, providing potential candidates for future validation of regulatory roles. In addition to providing spatial information, mass spectrometry imaging (MSI) technique enables the characterization of signaling molecules while preserving the temporal resolution. A novel MSI-based platform is developed by interfacing with microdialysis sample collection and is applied to the study of in vivo neuropeptide degradation profiles in an off-line ‘real-time’ fashion. This unique platform provides novel insights into neuropeptide inactivation/elimination process, which is an essential step to understand peptidegic signaling pathway. In addition to neuropeptides, this platform has been further modified to study secreted neurotransmitters, and small molecule metabolites that might interact with neuropeptides in crustacean for the first time. This work not only reports improvements upon neuropeptides identification and quantitation by developing improved analytical strategies, but also provides important evidence for the potential roles of several neuropeptides in regulating food intake and circadian rhythm behaviors. Novel platform that integrates MALDI-MSI with microdialysis in exploring neurochemical changes in dynamic biological events is also presented, which could be potentially applied to many other systems in future research. Collectively this dissertation research develops new analytical methods and improves our fundamental understanding of neuropeptide signaling.
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 484 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 Mass Spectrometry Methods and Applications for Functional Characterization of the Crustacean Neuropeptidome written by Kellen Lynn DeLaney and published by . This book was released on 2020 with total page 524 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neuropeptides are a diverse class of signaling molecules that are responsible for modulating numerous functions within the nervous system. They are challenging to study because, like most signaling molecules, they are present in low abundances in vivo and prone to rapid degradation. In this dissertation, multifaceted mass spectrometry (MS) methods are developed and implemented to characterize neuropeptides within crustacean model organisms. Decapod crustaceans are a useful model for understanding circuit dynamics due to their simplified nervous system, robust central pattern generators, and homology to higher-order organisms, including mammals. This work involves developing methods to improve the coverage of neuropeptides detected by implementing complementary separation and ionization techniques, the identification and reproducibility of neuropeptide analysis with optimized mass spectral acquisition parameters, and the accuracy of sequence information with software specifically designed for neuropeptide analysis. These methods are utilized to profile the neuropeptides present in the cardiac neuromuscular system that may be responsible for modulating heartbeat, as well as feeding-related neuropeptides in tissue and circulating fluid that may be implicated in generating rhythms related to chewing and filtering of food. Overall, this dissertation research develops improved methods for analyzing neuropeptides, demonstrates the utility of these methods for better understanding their functional roles within crustacean model organisms, and provides deeper insight into how these neuropeptides may be involved in modulating key central pattern generators and influencing circuit dynamics.
Download or read book Protein Analysis using Mass Spectrometry written by Mike S. Lee and published by John Wiley & Sons. This book was released on 2017-06-19 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents Practical Applications of Mass Spectrometry for Protein Analysis and Covers Their Impact on Accelerating Drug Discovery and Development Covers both qualitative and quantitative aspects of Mass Spectrometry protein analysis in drug discovery Principles, Instrumentation, Technologies topics include MS of peptides, proteins, and ADCs , instrumentation in protein analysis, nanospray technology in MS protein analysis, and automation in MS protein analysis Details emerging areas from drug monitoring to patient care such as Identification and validation of biomarkers for cancer, targeted MS approaches for biomarker validation, biomarker discovery, and regulatory perspectives Brings together the most current advances in the mass spectrometry technology and related method in protein analysis
Download or read book Characterizing Neural Tissues with Mass Spectrometry Imaging Via Enhanced Computational Approaches written by Tyler A. Zimmerman and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Neuropeptides affect the activity of the myriad of neuronal circuits in the brain. They are under tight spatial and chemical control and the dynamics of their release and catabolism directly modify neuronal network activity. Understanding neuropeptide functioning requires approaches to determine their chemical and spatial heterogeneity within neural tissue, but most imaging techniques do not provide the complete information desired. To provide chemical information, most imaging techniques used to study the nervous system require preselection and labeling of the peptides of interest; however, mass spectrometry imaging (MSI) detects analytes across a broad mass range without the need to target a specific analyte. When used with matrix-assisted laser desorption/ionization (MALDI), MSI detects analytes in the mass range of neuropeptides. MALDI MSI simultaneously provides spatial and chemical information resulting in images that plot the spatial distributions of neuropeptides over the surface of a thin slice of neural tissue. Here a variety of approaches for neuropeptide characterization are developed. Specifically, several computational approaches are combined with MALDI MSI to create improved approaches that provide spatial distributions and neuropeptide characterizations. After successfully validating these MALDI MSI protocols, the methods are applied to characterize both known and unidentified neuropeptides from neural tissues. The methods are further adapted from tissue analysis to be able to perform tandem MS (MS/MS) imaging on neuronal cultures to enable the study of network formation. In addition, MALDI MSI has been carried out over the timecourse of nervous system regeneration in planarian flatworms resulting in the discovery of two novel neuropeptides that may be involved in planarian regeneration. In addition, several bioinformatic tools are developed to predict final neuropeptide structures and associated masses that can be compared to experimental MSI data in order to make assignments of neuropeptide identities. The integration of computational approaches into the experimental design of MALDI MSI has allowed improved instrument automation and enhanced data acquisition and analysis. These tools also make the methods versatile and adaptable to new sample types.
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 Neuropeptides written by Adalberto Merighi and published by Humana Press. This book was released on 2017-04-30 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the early days, the field of neuropeptide biology has dramatically widened, and today the ultimate frontiers in neuropeptide research lie in the development of pharmacologically active compounds that are capable of crossing the blood-brain barrier to exert their biological role(s) in vivo and in the construction of genetic vectors to be employed in gene therapy. Neuropeptides: Methods and Protocols presents a readily reproducible collection of established and emerging techniques for neuropeptide research as contributed by expert researchers in the field. The detailed methods presented cover subjects such as immunocytochemical localization, biochemical characterization, functional analysis, development and production of genetic probes, and the design of neuropeptide derivatives for cellular neurobiology as well as the potential therapeutic applications. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and easy to follow, Neuropeptides: Methods and Protocols is intended for a large audience of scientists, including histologists, biochemists, cellular and molecular biologists, and electrophysiologists that are currently active in the field or are willing to enter this exciting and still expanding area of neurobiology.
Download or read book Integrating Supervised unsupervised Machine Learning and Molecular Modeling with Ion Mobility Mass Spectrometry written by Xueqin Pang (Ph.D.) and published by . This book was released on 2018 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the advantage of high processing speed and high sensitivity at low concentration, ion mobility mass spectrometry (IM-MS) has been increasingly employed in structural analysis of neuropeptides. However, the method's limitations, such as low structural resolution power, long-debated preservation of physiological structures in drift tube, prohibits its further application. In this dissertation, a novel multidisciplinary approach integrating supervised/unsupervised machine learning and molecular modeling in IM-MS was developed to help overcoming such limitations. Using molecular modeling, one could generate an ensemble of atomic resolution structure models in both gas phase and physiology (e.g. solution) phase. Then one could compare the modeled and measured CCS values, and thus connect each IM-MS arrival time distribution to specific atomic structure models. With supervised/unsupervised machine learning techniques, one could further identify the most representative structure of the peptide's functional structure, and identify the most critical interactions that result in a specific functional state. Structures of two classes of neuropeptides, Neuropeptide Y (NPY) and D-amino acid containing peptides (DAACPs), have been characterized using this new multidisciplinary approach. Successes have been made in illustrating the most representative biological structures, and thus pave the way to connect their unique functional roles starting from these structures.
