Download or read book Characterization of Macromolecular Systems by Mass Spectrometry and Hyphenated Techniques written by Sarah Charlotte Crotty and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The focus of this thesis was to gain in-depth structural information of synthetic polymers by the application of several combined techniques. The second chapter provides an overview about the influence of the polymer architecture on its characterization by mass spectrometry and complementary methods. In the third chapter, we demonstrate the use of MS, more specifically MALDI-ToF MS, which provides molar masses and dispersity values for poly(furfuryl glycidyl ether) (PFGE). The second example is the study of poly(N-isopropyl acrylamide) (PNiPAm) copolymers with glyco-monomers with specific combinations of matrices and cationization agents. The fourth chapter will combine three different examples regarding linear, star-shaped and hybrid polymers, which were analyzed by advanced techniques. The linear copolymers were analyzed by separating them according to their chemical heterogeneity using liquid absorption chromatography at critical conditions (LACCC) of poly(2-ethyl-2-oxazoline) (PEtOx), followed by automated spotting onto a MALDI target, which was subsequently analyzed by MALDI. Secondly, star-shaped polymers: [poly(ethylene oxide) (PEO)-b-PEtOx]8 were monitored firstly by using LACCC of linear PEO as first separation dimension and furthermore injected onto an SEC column confirming the molar mass. Lastly, a hybrid PEO star-shaped polymer was investigated using MALDI to verify the complete functionality of the core with PEO arms. Finally, the last chapter will focus on the creation of a software to obtain information regarding average composition, overcoming isotopic, overlapping peaks and isobaric species from MS spectra. Moreover, the quantitative studies were carried out by correction of the mass discrimination and isotopic abundance. Consequently, advanced analytical techniques such as different ionization techniques within MS, a range of chromatographic hyphenation and computational methods are implemented for elucidating the complexity of synthetic polymers.
Download or read book Native Mass Spectrometry and Complementary Techniques to Characterize Biological Macromolecular Assemblies written by Andrew S. Norris and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The structures adopted by biological macromolecules and macromolecular complexes are directly tied to their function. By better understanding the relationship between structure and function of biomolecules, lifesaving and life-changing interventions can be designed such as small molecule inhibitors of viral enzymes. Characterization of macromolecules with high-resolution structural techniques has greatly improved our fundamental understanding of how structures dictate function. High-resolution structural techniques including x-ray crystallography, cryo-electron microscopy, and nuclear magnetic resonance spectroscopy, however, have many challenges and so they require complementary techniques. Native mass spectrometry is one such technique that can be used to interrogate macromolecular assemblies and accurately determine molecular weight(s), oligomeric state(s), ligand-binding, and topology of the assembly. Native mass spectrometry has the advantage of not being limited by some of the common issues encountered by high-resolution techniques like molecular flexibility and sample heterogeneity that can limit resolution attainable or prevent structure determination altogether. This attribute is particularly valuable for the characterization of protein-nucleic acid complexes that have proven to be some of the more challenging complexes for high-resolution techniques. Throughout this work, native mass spectrometry is emphasized as a clear approach for examining differences in macromolecular assemblies that highlight the structural diversity of macromolecular systems which would otherwise not be evident. Chapter 3 describes identification of the physiological protein interface of a plant protein, BX1.This approach demonstrates the use of native mass spectrometry and covalent cross-linking mass spectrometry to solve a common issue with X-ray crystallography, namely artificial protein contacts formed during the crystallization process. Chapter 4 describes the investigation of the assembly pathway for RNase P, a multi-subunit archaeal ribonucleoprotein. Additionally, native mass spectrometry addresses the absence of a protein subunit in the cryo-EM structure of the same RNase P. Chapter 5 describes the investigation of the different assembly states of DNA annealing proteins. A cryo-EM reconstruction of a section of one of the protein-DNA complexes was determined. For this protein, native mass spectrometry complemented the cryo-EM study by determining the composition of the entire complex. With the native mass spectrometry assembly data for DNA annealing proteins and the cryo-EM for one of these proteins, proposed revisions to the current model of single-strand annealing are presented. Finally, in Chapter 6, cooperative ligand binding of three cyclic homo-oligomers is reported and a cooperative binding model, the nearest-neighbor model, was used to fit the data to quantitively determine thermodynamic parameters. RNA binding was also tested, but work is still ongoing. Overall, the work presented herein demonstrates the use of native mass spectrometry to study the assembly states of macromolecular complexes and hereby gain insights not easily accessible by other structural techniques.
Download or read book Mass Spectrometry in Biology Medicine written by A.L. Burlingame and published by Springer Science & Business Media. This book was released on 1999-09-14 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt: Leading practitioners detail revolutionary new spectrometric techniques for the identification and covalent structural characterization of macromolecules, proteins, glycoconjugates, and nucleic acids. Based on the Fourth International Symposium on Mass Spectrometry in the Health and Life Sciences held in San Francisco in 1998, this invaluable book contains tested strategies for solving many significant biomedical research problems. The techniques use mass spectrometry, automated computer processing of spectral information, and gene, protein, and EST databases for genomic and proteomic correlations. Mass Spectrometry in Biology and Medicine offers a unique opportunity to explore and apply these new techniques of mass spectrometry that are revolutionizing the identification and structural characterization of proteins, carbohydrates, and nucleic acids.
Download or read book Tandem Mass Spectrometry written by Ana Varela Coelho and published by BoD – Books on Demand. This book was released on 2013-05-29 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tandem Mass Spectrometry - Molecular Characterization presents a comprehensive coverage of theory, instrumentation and description of experimental strategies and MS/MS data interpretation for the structural characterization of relevant molecular compounds. The areas covered include the analysis of drugs, metabolites, carbohydrates and protein post-translational modifications. The book series in Tandem Mass Spectrometry serves multiple groups of audiences; professional (academic and industry), graduate students and general readers interested in the use of modern mass spectrometry in solving critical questions of chemical and biological sciences.
Download or read book Mass Spectrometry in the Analysis of Large Molecules written by Catherine McNeal and published by . This book was released on 1986-12-19 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ten lectures plus several contributions examine the progress made in the analysis of large molecules of m/z 10,000 and beyond. Explores how to apply this technology and ways of extending the analysis to even higher masses. Also examines how mass spectrometry techniques fit in with existing chemical and biochemical methods of structure analysis.
Download or read book Structural Analysis of Macromolecular Complexes Using Electrospray Ionization Mass Spectrometry Based Approaches written by Jingshu Guo and published by . This book was released on 2013 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) has become one of the most robust, reliable and widely used analytical techniques in scientific research due to factors like its speed of analysis, ease of operation, high sensitivity, and applicability to a broad range of analytes. The development of the so-called "soft" ionization methods electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) played a pivotal role in the application of MS to biochemical and biophysical fields enabling comprehensive studies of biomolecules, macromolecules and their complexes. This dissertation presents method development and the application of MS-based strategies for complete sequence and structure determination of hemoglobin (Hb); investigation of the interaction between human Hb and Band 3; characterization of the interaction between Alanyl-tRNA synthetase with tRNA and various ligands; and characterization of various thiol-protected silver nanoclusters. First, the complete primary amino acid sequences of hemoglobin from the endangered species snow leopard (Uncia uncia), Amur tiger (Panthera tigris altaica), Cheetah (Acinonyx jubatus) and Francois' Langur (Trachypithecus francoisi) were determined using a combination of the bottom-up approach to proteomics in combination with single crystal X-ray diffraction. In this approach, MS was used to provide on average 70% coverage of the sequences, which was used in refinement of the diffraction data. The electron density maps from the diffraction data were used to determine the parts of the sequences not covered by MS as well as differentiate between isomeric residues. During the refinement of the X-ray diffraction data, a unique conformational state, the Bform, for naturally occurring ligated hemoglobin was discovered in two feline Hbs. Structural comparisons and possible biological relevance for the B-form will be presented. The binding of human hemoglobin to synthetic peptides corresponding to the Hb-binding sites of human erythrocyte Band 3 is also presented. The effects on binding of ligation and oxidation state of normal human HbA; human sickle HbS; Hb-binding site and peptide length; and Band 3 N-terminal acetylation were investigated. The optimization of MS instrumental parameters and solution conditions for stabilizing and protecting labile thiol-protected silver nanoclusters through ionization, mass analysis and detection is presented. The relatively much more stable and well characterized gold-glutathione cluster Au25(SG)18 was used as a model for instrumental optimization (SG, glutathione). The most crucial instrumental parameters to protecting the clusters were cone gas flow rate, trap/transfer collision energy, and source temperature. Using these optimized parameters and adjustment of solution conditions led to the formula assignment for Ag32(SG)19, the species isolated from band 6 of a polyacrylamide gel electrophoretic separation. Using a similar approach the formula assignment for Ag44L30-4 (L, p-mercaptobenzoic acid) was confirmed. Collision induced dissociation (CID) studies were used to demonstrate that Ag43L28-3, another abundant species in the mass spectra was in fact a fragment of the intact cluster from the facile loss of AgL2-. CID and ion mobility mass spectrometry (IMMS) of Au25(SG)18, Ag32(SG)19, and Ag44L30-4 were used to gain insight into the surface structure and stability of the fragile silver clusters. Finally, the 3'-tRNA binding site on E. coli Alanyl-tRNA synthetase was identified by first crosslinking the 3'-periodate-oxidized tRNAala to the enzyme followed by the bottom-up MS sequencing. Modified lysine residues identified were 74, 526 585, 637, 739 and 648. Lys 74 was in the aminoacylation domain while 526 585, 637, 739 and 648 were in the editing domain. These results highlight an alteration of the 3'-terminal of tRNAala interaction with the enzyme. To study the stability ARS with various ligands, non-hydrolysable adenylate analogs, ASAd and GSAd, were used. Data shows that complete binding of ASAd and GSAd was achieved and that binding occurred in a 1:1 stoichiometry. Binding of ASAd, the analog of the cognate ligand, stabilizes the enzyme against changes in solution pH relative to the apo-enzyme and the enzyme with GSAd bound.
Download or read book MALDI Mass Spectrometry for Synthetic Polymer Analysis written by Liang Li and published by John Wiley & Sons. This book was released on 2009-10-22 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: Principles and Practices of Polymer Mass Spectrometry helps readers acquire the skills necessary for selecting the optimal methods, handling samples, analyzing the data, and interpreting the results of the mass spectrometry of polymers. This guide describes the principles of polymer MS and best practices in polymer characterization. It discusses different approaches, including MALDI, ESI, TOF MS, and FT-MS. It provides a guide to developing appropriate sample preparation protocols for different polymers. Complete with examples of applications and experiments, this is an excellent reference for scientists, researchers, graduate students, and others.
Download or read book Fundamentals of Contemporary Mass Spectrometry written by Chhabil Dass and published by John Wiley & Sons. This book was released on 2007-05-11 with total page 512 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern mass spectrometry - the instrumentation and applications in diverse fields Mass spectrometry has played a pivotal role in a variety of scientific disciplines. Today it is an integral part of proteomics and drug discovery process. Fundamentals of Contemporary Mass Spectrometry gives readers a concise and authoritative overview of modern mass spectrometry instrumentation, techniques, and applications, including the latest developments. After an introduction to the history of mass spectrometry and the basic underlying concepts, it covers: Instrumentation, including modes of ionization, condensed phase ionization techniques, mass analysis and ion detection, tandem mass spectrometry, and hyphenated separation techniques Organic and inorganic mass spectrometry Biological mass spectrometry, including the analysis of proteins and peptides, oligosaccharides, lipids, oligonucleotides, and other biological materials Applications to quantitative analysis Based on proven teaching principles, each chapter is complete with a concise overview, highlighted key points, practice exercises, and references to additional resources. Hints and solutions to the exercises are provided in an appendix. To facilitate learning and improve problem-solving skills, several worked-out examples are included. This is a great textbook for graduate students in chemistry, and a robust, practical resource for researchers and scientists, professors, laboratory managers, technicians, and others. It gives scientists in diverse disciplines a practical foundation in modern mass spectrometry.
Download or read book Mass Spectrometry in Structural Biology and Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2012-04-03 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biology, and biopharmaceuticals, the book is a practical guide to understanding the role of MS techniques in biophysical research. Designed to meet the needs of both academic and industrial researchers, it makes mass spectrometry accessible to professionals in a range of fields, including biopharmaceuticals. This new edition has been significantly expanded and updated to include the most recent experimental methodologies and techniques, MS applications in biophysics and structural biology, methods for studying higher order structure and dynamics of proteins, an examination of other biopolymers and synthetic polymers, such as nucleic acids and oligosaccharides, and much more. Featuring high-quality illustrations that illuminate the concepts described in the text, as well as extensive references that enable the reader to pursue further study, Mass Spectrometry in Structural Biology and Biophysics is an indispensable resource for researchers and graduate students working in biophysics, structural biology, protein chemistry, and related fields.
Download or read book Mass Spectrometry in Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2005-05-06 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first systematic summary of biophysical mass spectrometrytechniques Recent advances in mass spectrometry (MS) have pushed the frontiersof analytical chemistry into the biophysical laboratory. As aresult, the biophysical community's acceptance of MS-based methods,used to study protein higher-order structure and dynamics, hasaccelerated the expansion of biophysical MS. Despite this growing trend, until now no single text has presentedthe full array of MS-based experimental techniques and strategiesfor biophysics. Mass Spectrometry in Biophysics expertly closesthis gap in the literature. Covering the theoretical background and technical aspects of eachmethod, this much-needed reference offers an unparalleled overviewof the current state of biophysical MS. Mass Spectrometry inBiophysics begins with a helpful discussion of general biophysicalconcepts and MS-related techniques. Subsequent chaptersaddress: * Modern spectrometric hardware * High-order structure and dynamics as probed by various MS-basedmethods * Techniques used to study structure and behavior of non-nativeprotein states that become populated under denaturingconditions * Kinetic aspects of protein folding and enzyme catalysis * MS-based methods used to extract quantitative information onprotein-ligand interactions * Relation of MS-based techniques to other experimental tools * Biomolecular properties in the gas phase Fully referenced and containing a helpful appendix on the physicsof electrospray mass spectrometry, Mass Spectrometry in Biophysicsalso offers a compelling look at the current challenges facingbiomolecular MS and the potential applications that will likelyshape its future.
Download or read book Molecular Characterization of Polymers written by Muhammad Imran Malik and published by Elsevier. This book was released on 2021-03-09 with total page 670 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Characterization of Polymers presents a range of advanced and cutting-edge methods for the characterization of polymers at the molecular level, guiding the reader through theory, fundamentals, instrumentation, and applications, and supporting the end goal of efficient material selection and improved material performance. Each chapter focuses on a specific technique or family of techniques, including the different areas of chromatography, field flow fractionation, long chain branching, static and dynamic light scattering, mass spectrometry, NMR, X-Ray and neutron scattering, polymer dilute solution viscometry, microscopy, and vibrational spectroscopy. In each case, in-depth coverage explains how to successfully implement and utilize the technique. This practical resource is highly valuable to researchers and advanced students in polymer science, materials science, and engineering, and to those from other disciplines and industries who are unfamiliar with polymer characterization techniques. Introduces a range of advanced characterization methods, covering aspects such as molecular weight, polydispersity, branching, composition, and tacticity Enables the reader to understand and to compare the available technique, and implement the selected technique(s), with a view to improving properties of the polymeric material Establishes a strong link between basic principles, characterization techniques, and real-life applications
Download or read book Characterization of Structure and Dynamics of Macromolecular Systems by NMR Methods written by International Union of Pure and Applied Physics. Macromolecular Division and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Development of Top down Mass Spectrometry Methods for Structural Characterization of Protein Macromolecules Utilizing 193nm Ultraviolet Photodissociation written by Michael B. Cammarata and published by . This book was released on 2016 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: The dissertation will discuss the advancement of informative structural biology techniques utilizing a top-down centric workflow with 193nm ultraviolet photodissociation (UVPD) mass spectrometry. Native electrospray ionization is used to transport proteins to the gas phase in a native-like state, then UVPD is used for structural characterization to reveal ligand binding sites within a protein-ligand complex as well as detect conformational changes based upon the suppression or enhancement of backbone cleavages. Conformational changes induced by ligand exchange or removal and single amino acid mutations as well as combinations of the two (ligands and mutations) are investigated. The rich fragmentation patterns of UVPD are also used for structural characterization of crosslinked proteins. Typically these crosslinking experiments are performed by bottom-up mass spectrometry with has significant shortcomings. The main drawback is the need for proteolysis which cuts proteins into small peptides, thus increasing the complexity of the samples and its subsequent analysis. Additionally this proteolysis step loses the post-translation modification information or amino acid mutations that may be driving a specific protein-protein interaction. Top-down methods avoid protein digestion and thus are used to directly evaluate the protein interactions or protein complexes. These two methodologies will bring the mass spectrometry and structural biology community a step closer to the realization of high-throughput structural biology for proteins and their interactions with other proteins and small molecules.
Download or read book Mass Spectrometry Methods for Enhanced Characterization of Biological Systems written by Lisa Rachel Szymkowicz and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: As the pharmaceutical industry moves towards larger protein-based therapeutics over chemically synthesized small molecules, there are increasing demands for parallel advancement in the technologies used for quality control of these biologically-derived products (biopharmaceuticals). This work describes the implementation of mass spectrometry (MS)-based methods in three areas where MS is well-positioned to fulfill unmet analytical needs. First, time-resolved electrospray ionization hydrogen-deuterium exchange (TRESI-HDX) and ion mobility spectroscopy (IMS)-MS were used to study conformational dynamics in transient Cytochrome c-lipid interactions. MS was also implemented for proteomic characterization of in-process and purified samples from acellular Pertussis vaccines. Further development of a targeted MS method is described for quantitation of two residual protein toxins, adenylase cyclase toxin (ACT) and dermoneucrotic toxin (DNT), and a glycopeptide, tracheal cytotoxin (TCT), from Bordetella pertussis. Collectively, the results highlight advancement in the application of structural and quantitative proteomics for more effective characterization of next generation biopharmaceuticals.
Download or read book Mass Spectrometry Methods For Macromolecules written by Kevin J Endres and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation describes the development of novel mass spectrometry (MS) methodologies and techniques to improve, simplify and allow for specific characterizations of synthetic materials. Successful MS analyses are governed by the mass spectrometry principles surrounding specific ionization sources, mass analyzers and ion detecters. The methods described within this dissertation provide information about polymer materials that is historically difficult to determine using other available analytical techniques. Self-assembled terpyridine (tpy)-based metallomacrocycles that are coordinatively-bound using various transition metals were investigated through the analysis of their collision cross-section (CCS) values obtained by travelling wave ion mobility (TWIM)-MS separation, and through comparison to modeled/simulated structures and theoretical CCS values. This work demonstrated the uniquely powerful ability of TWIM-MS separation for architectural verification in samples containing stoichiometrically-defined isobaric ion species ranging from dimeric macrocycles to hexameric macrocycles. Furthermore, TWIM-MS was utilized in a separate project which allowed for the development of a method to monitor concentration dependent supramolecular structural equilibria and conformational trends. Using the methodology in this work, equilibrium constants were derived from these data; this was illustrated for two equilibria concerning the self-assembly of a tpy-based ligand containing a flexible crown ether moiety with Zn2+ ions, and a tetrakisterpyridinyl ligand with Cd2+ ions, which have previously been shown to reversibly interconvert. Additionally, experimental CCS values were also derived from drift time measurements and compared with theoretical predictions for these complex self-assembled terpyridine-based supramolecules to provide insight into their size, stoichiometry and architecture. Parallel studies have focused on the development of methods that can obtain connectivity and compositional information about covalently cross-linked polymers. The atmospheric solids analysis probe (ASAP) ionization source has been combined with MS, tandem MS (MS/MS) and TWIM to create an effective top-down technique for the molecular characterization of the mentioned materials, which were utilized in this project to address persisting structural questions about synthetic polymer cross-linking microstructures. The structural insight gained from these studies was illustrated by the analysis of two hydrogels: 1) oxime cross-linked poly(ethylene glycol) (PEG) hydrogels formed from the click-reaction between 4-arm PEG star polymers with levulinamide or levulinic acid end group functionalities and 4-arm PEG star polymers with aminoxyacetaamide or aminooxyacetic acid end group functionalities, and 2) cross-linked poly(methacrylate) (PMA)-PEG hydrogels formed from PEGdimethacrylate (PEGDMA) polymerized via radical propagation in the presence of a lithium acylphosphazine (LAP) photoinitiator and ultraviolet (UV) light. Lastly, the design of a surface-specific imaging technique with a probing depth of
Download or read book Mass Spectrometry in Polymer Chemistry written by Christopher Barner-Kowollik and published by John Wiley & Sons. This book was released on 2012-01-27 with total page 501 pages. Available in PDF, EPUB and Kindle. Book excerpt: Combining an up-to-date insight into mass-spectrometric polymer analysis beyond MALDI with application details of the instrumentation, this is a balanced and thorough presentation of the most important and widely used mass-spectrometric methods. Written by the world's most proficient experts in the field, the book focuses on the latest developments, covering such technologies and applications as ionization protocols, tandem and liquid chromatography mass spectrometry, gas-phase ion-separation techniques and automated data processing. Chapters on sample preparation, polymer degradation and the usage of mass-spectrometric tools on an industrial scale round off the book. As a result, both entrants to the field and experienced researchers are able to choose the appropriate methods and instrumentations -- and to assess their respective strengths and limitations -- for the characterization of polymer compounds.
Download or read book Biofunctional Molecule Discovery and Characterization Via Multifaceted Mass Spectrometry Approaches written by Qinjingwen Cao and published by . This book was released on 2019 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biofunctional molecules, such as neurotransmitters, metabolites and neuropeptides, are involved in various biological and regulatory processes and play essential roles in vivo. Owing to their complex structures and wide range of concentrations, analyzing those molecules in complex biological matrices has been challenging, and it is highly desirable to develop selective and sensitive analytical methodologies to achieve efficient characterization. In this dissertation, both liquid chromatography-mass spectrometry (LC-MS) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) methods were developed to identify and characterize biofunctional molecules. Specifically, an LC-MS workflow was developed to determine neurotransmitters and metabolites with a reference tandem mass spectrometry library. Moreover, an enrichment-free method has been applied to discover N-linked and O-linked glycosylation on crustacean neuropeptides. Additionally, this work demonstrates complementary MALDI MSI approaches to map in situ neurotransmitter distribution on high resolution-accurate mass Orbitrap platform. The employment of sub-atmospheric pressure MALDI MSI has featured the alleviation of ion suppression effects and produced high resolution molecular imaging of neuropeptides and lipids in vivo. Overall, this work not only improves multifaceted analytical techniques for uncovering the complexity of crustacean signaling molecules but also provides potential applications in a broad set of biological systems.
