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Top Down Characterization Of Proteins By Electron Capture Dissociation And Blackbody Infrared Radiative Dissociation Mass Spectrometry
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Book Synopsis Top Down Characterization of Proteins by Electron Capture Dissociation and Blackbody Infrared Radiative Dissociation Mass Spectrometry by : Ying Ge
Download or read book Top Down Characterization of Proteins by Electron Capture Dissociation and Blackbody Infrared Radiative Dissociation Mass Spectrometry written by Ying Ge and published by . This book was released on 2002 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mass Spectrometry for Microbial Proteomics by : Haroun N. Shah
Download or read book Mass Spectrometry for Microbial Proteomics written by Haroun N. Shah and published by John Wiley & Sons. This book was released on 2010-10-28 with total page 545 pages. Available in PDF, EPUB and Kindle. Book excerpt: New advances in proteomics, driven largely by developments in mass spectrometry, continue to reveal the complexity and diversity of pathogenic mechanisms among microbes that underpin infectious diseases. Therefore a new era in medical microbiology is demanding a rapid transition from current procedures to high throughput analytical systems for the diagnosis of microbial pathogens. This book covers the broad microbiological applications of proteomics and mass spectrometry. It is divided into six sections that follow the general progression in which most microbiology laboratories are approaching the subject –Transition, Tools, Preparation, Profiling by Patterns, Target Proteins, and Data Analysis.
Book Synopsis Top-Down Mass Spectrometry Characterization of Protein-Ligand Complexes Important to Neurodegenerative Diseases by : Piriya Wongkongkathep
Download or read book Top-Down Mass Spectrometry Characterization of Protein-Ligand Complexes Important to Neurodegenerative Diseases written by Piriya Wongkongkathep and published by . This book was released on 2015 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) has made significant contributions to protein and proteomics analysis during the past decades from its advantages of speed, sensitivity, specificity, and low sample consumption. While the proteomics field grows rapidly to identify thousands of proteins in a single analysis, "native" mass spectrometry, exploiting the unique features of electrospray ionization (ESI) for delivering large macromolecules to the mass spectrometer, has provided many potential exciting capabilities and applications to structural biology and biochemistry. It can analyze proteins in their native states, i.e., structures present in their native configurations from physiological pH solutions, with minimal sample preparation. In this thesis, I describe the application of native ESI combined with top-down MS using electron capture dissociation (ECD) and ion mobility (IM) to characterize the molecular features of protein-ligand complexes. Binding and structural information can be comprehensively obtained from this experimental platform. Native ESI-MS alone provides molecular mass, stoichiometry, and binding affinity, all from a single analysis. We demonstrate that top-down MS, the fragmentation of intact proteins and protein complexes using MS, offers a powerful capability to elucidate the location of ligand binding on a protein's structure and for probing the surface topology of proteins. Ion mobility mass spectrometry, a recently developed technique that yields information on the structural conformation of molecules, was used to reveal structural changes of proteins upon ligand binding. My thesis focuses on several proteins, including -synuclein (AS), which is a small protein related to Parkinson's disease. AS is natively unfolded at physiological pH, which makes it difficult to study by standard methods such as X-ray crystallography or NMR. Using our mass spectrometry techniques, transition metal binding (copper, cobalt, and manganese) to AS that is associated with accelerating fibril formation was monitored. The binding of a small molecule amyloid inhibitor called molecular tweezer (MT or CLR01) on two model proteins important in neurodegenerative diseases, AS and superoxide dismutase (SOD1), was studied. Tandem mass spectrometry (MS/MS) techniques such as collisionally activated dissociation (CAD) along with ECD were used to characterize the sites of binding of small molecule ligands to proteins. Ion mobility mass spectrometry was implemented to reveal the conformational changes of AS upon metal binding. It was demonstrated that copper can induce the AS protein to collapse into a more compact state, which may provide a hint of the mechanisms behind amyloid fibrillation. Additionally, two new methods to extend the application of top-down MS for protein structure characterization were developed. First, the same molecular tweezer molecule, which has a specificity to bind lysine residues, was used to probe surface residues of proteins. The lysines found to bind to the molecular tweezers identified by top-down MS correlates well with solvent accessibility values, suggesting that the MT compound can be applied as a molecular probe to pinpoint surface active lysine residues. Lastly, supplemental activation methods by ultraviolet and infrared laser irradiation prior to ECD was applied to assist disulfide bond cleavage of complex multiple intermolecular and intramolecular disulfide bond-containing proteins. Backbone bond cleavage from top-down MS was significantly increased when the disulfide bonds were cleaved, allowing more sequence information to be obtained. The new methods described in this thesis extend the applicability of mass spectrometry to provide a more complete picture of a protein's structure.
Book Synopsis Application of Top Down Mass Spectrometry to Mechanistic Enzymology, Protein Folding, and Protein Modificaton Kinetics by : Huili Zhai
Download or read book Application of Top Down Mass Spectrometry to Mechanistic Enzymology, Protein Folding, and Protein Modificaton Kinetics written by Huili Zhai and published by . This book was released on 2005 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Electrospray and MALDI Mass Spectrometry by : Richard B. Cole
Download or read book Electrospray and MALDI Mass Spectrometry written by Richard B. Cole and published by John Wiley & Sons. This book was released on 2011-09-26 with total page 900 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discover how advances in mass spectrometry are fueling new discoveries across a broad range of research areas Electrospray and MALDI Mass Spectrometry brings both veteran practitioners and beginning scientists up to date with the most recent trends and findings in electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. In particular, this Second Edition highlights how advances in electrospray and MALDI mass spectrometry are supporting important discoveries in new and emerging fields such as proteomics and metabolomics as well as in traditional areas of chemistry and physics research. Electrospray AND MALDI Mass Spectrometry, SECOND EDITION is divided into five parts: Part A, Fundamentals of ES, explains the fundamental phenomena underlying the electrospray process, including selectivity in ionization and inherent electrochemistry, and concludes with a chapter offering a comparative inventory of source hardware Part B, Fundamentals of MALDI, confronts ionization mechanisms, instrument development, and matrix selection, and includes a final chapter that explores the special application of MALDI to obtain two-dimensional images of spatial distributions of compounds on surfaces Part C, ES and MALDI Coupling to Mass Spectrometry Instrumentation, examines the coupling of these ionization techniques to various mass analyzers, including quadrupole ion trap, time-of-flight, Fourier transform ion cyclotron resonance, and ion mobility mass spectrometers Part D, Practical Aspects of ES and MALDI, investigates analytical issues including quantification, charge-state distributions, noncovalent interactions in solution that are preserved as gas-phase ions, and various means of ion excitation in preparation for tandem mass spectrometry, and offers a guide to the interpretation of even-electron mass spectra Part E, Biological Applications of ES and MALDI, examines the role of mass spectrometry in such areas as peptide and protein characterization, carbohydrate analysis, lipid analysis, and drug discovery Written by a team of leading experts, the book not only provides a critical review of the literature, but also presents key concepts in tutorial fashion to help readers take full advantage of the latest technological breakthroughs and applications. As a result, Electrospray and MALDI Mass Spectrometry will help researchers fully leverage the power of electrospray and MALDI mass spectrometry. The judicious compartmentalization of chapters, and the pedagogic presentation style throughout, render the book highly suitable for use as a text for graduate-level courses in advanced mass spectrometry.
Book Synopsis Practical Aspects of Trapped Ion Mass Spectrometry, Volume V by : Raymond E. March
Download or read book Practical Aspects of Trapped Ion Mass Spectrometry, Volume V written by Raymond E. March and published by CRC Press. This book was released on 2016-04-19 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: Widely used in medical research, pharmaceutical and fine chemicals industries, biological and physical sciences, and security and environmental agencies, mass spectrometry techniques are continually under development. In Practical Aspects of Trapped Ion Mass Spectrometry: Volume V, Applications of Ion Trapping Devices, an international panel of aut
Book Synopsis Enhanced Protein Characterization Through Selective Derivatization and Electrospray Ionization Tandem Mass Spectrometry by : Lisa Anne Vasicek
Download or read book Enhanced Protein Characterization Through Selective Derivatization and Electrospray Ionization Tandem Mass Spectrometry written by Lisa Anne Vasicek and published by . This book was released on 2011 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: There continue to be great strides in the field of proteomics but as samples become more complex, the ability to increase sequence coverage and confidence in the identification becomes more important. Several methods of derivatization have been developed that can be used in combination with tandem mass spectrometry to identify and characterize proteins. Three types of activation, including infrared multiphoton dissociation, ultraviolet photodissociation, and electron transfer dissociation, are enhanced in this dissertation and compared to the conventional method of collisional induced dissociation (CID) to demonstrate the improved characterization of proteins. A free amine reactive phosphate group was synthesized and used to modify the N-terminus of digested peptides. This phosphate group absorbs at the IR wavelength of 10.6 [mu]m as well as the Vacuum-ultraviolet (VUV) due to an aromatic group allowing modified peptides to be dissociated by infrared multi-photon dissociation (IRMPD) or ultraviolet photodissociation (UVPD) whereas peptides without this chromophore are less responsive to IR or UV irradiation. The PD spectra for these modified peptides yield simplified MS/MS spectra due to the neutralization of all N-terminal product ions from the incorporation the negatively charged phosphate moiety. This is especially advantageous for UVPD due to the great number of product ions produced due to the higher energy deposition of the UV photons. The MS/MS spectra also produce higher sequence coverage in comparison to CID of the modified or unmodified peptides due to more informative fragmentation pathways generated upon PD from secondary dissociation and an increased ion trapping mass range. IRMPD is also implemented for the first time on an orbitrap mass spectrometer to achieve high resolution analysis of IR chromophore-derivatized samples as well as top-down analysis of unmodified proteins. High resolution/high mass accuracy analysis is extremely beneficial for characterization of complex samples due to the likelihood of false positives at lower resolutions/accuracies. For electron transfer dissociation, precursor ions in higher charge states undergo more exothermic electron transfer and thus minimize non-dissociative charge reduction. In this dissertation, cysteine side chains are alkylated with a fixed charge to deliberately increase the charge states of peptides and improve electron transfer dissociation. ETD can also be used to study protein structure by derivatizing the intact structure with a hydrazone reagent. A hydrazone bond will be preferentially cleaved during ETD facilitating the recognition of any modified residues through a distinguishing ETD fragmentation spectrum.
Book Synopsis Advancing Intact Protein Analysis by Top-down Mass Spectrometry by : Bifan Chen
Download or read book Advancing Intact Protein Analysis by Top-down Mass Spectrometry written by Bifan Chen and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of proteins is critical for understanding cellular functions at the molecular level. Top-down mass spectrometry (MS) has emerged as a premier tool for global and comprehensive analysis of proteoforms. The top-down approach retains intact mass information, providing a "bird's-eye" view of the proteome and allowing for identification of novel proteoforms, in-depth sequence characterization, and quantification of disease associated post-translational modifications (PTMs). However, many technical challenges still exist. The research described here involves analytical development in top-down MS, particularly in the areas of enrichment, separation, and characterization of samples ranging from standard proteins and complex lysates, to large therapeutic biomolecules. Chapter 1 provides an introduction and review of recent advances in different aspects of top-down proteomics. Chapters 2 and 3 are related to the study of intact phosphoproteins. Specifically, chapter 2 describes the use of functionalized nanoparticles for enrichment and the subsequent coupling of online liquid chromatography (LC)-MS for characterizing endogenous phosphoproteins from complex cell lysates. Chapter 3 investigates how phosphorylation moieties might influence the efficiency of electron capture dissociation (ECD). Chapters 4 and 5 focus on the development of hydrophobic interaction chromatography (HIC) that could be coupled online directly with MS and its applications to therapeutic molecules (monoclonal antibodies). Chapter 6 describes a middle-down approach to obtain multi-attribute of both cysteine and lysine conjugated antibody-drug conjugates, which overcomes some current challenges using HIC-MS and the top-down approach. Overall, these analytical developments expand the toolbox of the top-down approach and generally facilitate the analysis of intact proteins.
Book Synopsis Mass Spectrometry by : Agnieszka Kraj
Download or read book Mass Spectrometry written by Agnieszka Kraj and published by John Wiley & Sons. This book was released on 2008-12-01 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: With contributions from noted experts from Europe and North America, Mass Spectrometry Instrumentation, Interpretation, and Applications serves as a forum to introduce students to the whole world of mass spectrometry and to the many different perspectives that each scientific field brings to its use. The book emphasizes the use of this important analytical technique in many different fields, including applications for organic and inorganic chemistry, forensic science, biotechnology, and many other areas. After describing the history of mass spectrometry, the book moves on to discuss instrumentation, theory, and basic applications.
Book Synopsis The Encyclopedia of Mass Spectrometry by : Michael L. Gross
Download or read book The Encyclopedia of Mass Spectrometry written by Michael L. Gross and published by . This book was released on 2006-10-30 with total page 1098 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents information on the biographies of recognized pioneers and innovators in the field of mass spectrometry. - Highlights over 120 innovators in mass spectrometry, including several Nobel Prize winners. Discusses instrumentation and their uses, also providing interesting information on the careers, characters, and life stories of the people who did the work. Offers unique insight into the careers and personalities of luminaries in the field.
Book Synopsis Strategies for Protein and Peptide Characterization and Quantification Using Electron-transfer Dissociation Mass Spectrometry and Intrinsic Fluorescence by :
Download or read book Strategies for Protein and Peptide Characterization and Quantification Using Electron-transfer Dissociation Mass Spectrometry and Intrinsic Fluorescence written by and published by . This book was released on 2012 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: STRATEGIES FOR PROTEIN AND PEPTIDE CHARACTERIZATION AND QUANTIFICATION USING ELECTRON-TRANSFER DISSOCIATION MASS SPECTROMETRY AND INTRINSIC FLUORESCENCE Jason D. Russell Under the supervision of Associate Professor Joshua J. Coon At the University of Wisconsin-Madison The following chapters detail strategies for peptide and protein sequence analysis featuring electron-transfer dissociation (ETD) tandem mass spectrometry (MS/MS) and quantification using ultraviolet light-induced intrinsic fluorescence (UV-IF). Chapter 1 provides a brief background and overview. Chapter 2 discusses the optimization of the ETD MS/MS duty cycle for large-scale shotgun experiments. In Chapter 3, the first comprehensive analysis of peptide anions using negative ETD (NETD) is detailed. I report in Chapter 4 on the performance of an ion-ion reaction cell for intact protein analysis using large precursor populations for ETD MS/MS. The application of UV-IF for peptide detection and quantification using a custom fluorescence excitation and detection device is discussed in Chapter 5. An analysis of intact proteins from the 26S proteasome of Arabidopsis using top-down mass spectrometry and quantification by UV-IF is described in Chapter 6. In coordination with the Wisconsin Initiative for Science Literacy (WISL), Chapter 7 is a general description of my graduate research intended for non-specialists in an effort to promote science literacy in the broader community.
Book Synopsis Ewing's Analytical Instrumentation Handbook, Fourth Edition by : Nelu Grinberg
Download or read book Ewing's Analytical Instrumentation Handbook, Fourth Edition written by Nelu Grinberg and published by CRC Press. This book was released on 2019-02-21 with total page 1614 pages. Available in PDF, EPUB and Kindle. Book excerpt: This handbook is a guide for workers in analytical chemistry who need a starting place for information about a specific instrumental technique. It gives a basic introduction to the techniques and provides leading references on the theory and methodology for an instrumental technique. This edition thoroughly expands and updates the chapters to include concepts, applications, and key references from recent literature. It also contains a new chapter on process analytical technology.
Book Synopsis Methodologies and Applications for the Analysis of Intact Proteins and Protein-ligand Interactions by Top-down Mass Spectrometry by : Michael Nshanian
Download or read book Methodologies and Applications for the Analysis of Intact Proteins and Protein-ligand Interactions by Top-down Mass Spectrometry written by Michael Nshanian and published by . This book was released on 2018 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advent of top-down protein mass spectrometry (MS), or direct analysis of intact proteins forgoing proteolysis, has transformed the field of protein mass spectrometry, ushering in a new era of protein identification and characterization together with a new set of challenges. The analysis of intact proteins and their direct fragmentation in tandem (MS/MS) mode helps overcome the "inference" problem associated with peptide-based bottom-up proteomics; that is, correctly assigning given peptide fragments and their modifications to the intact protein from which they originated. Despite its many advantages, however, the top-down approach requires extensive sample fractionation and suffers from low sensitivity but much progress has been made. From recently-developed cross-linked polyacrylamide gels, from which intact proteins can be more easily recovered, to the discovery of reagents that enhance protein charging in electrospray ionization (ESI), there have been considerable gains in detection and sensitivity, offering the potential for a more complete and accurate characterization of a "proteoform": the full complement of the combinatorial possibilities that could arise from a given gene product. Top-down MS also includes the study of proteins in their native or native-like states. This is especially important in characterizing disease-related proteins, particularly in the context of protein aggregation. Native MS, using electron-capture dissociation (ECD) and ion mobility spectrometry (IMS), enables the study of protein-inhibitor complexes in the gas phase, offering structural insight into stoichiometry, site of inhibitor binding and mechanism of inhibition. In addition, intact analysis and electron-based fragmentation enable the detection of thermally-labile post-translational modifications like phosphorylation, known to play key regulatory roles in shifting proteins towards cytotoxic states. Top-down method developments in protein recovery, separation and supercharging have led to improvements in detection and sensitivity, while top-down MS applications to structural characterization of disease-related proteins have shed more light on the mechanisms of cytotoxic aggregation, offering greater promise of therapeutic development.
Book Synopsis Development of Top-down Mass Spectrometry Methods for Structural Characterization of Protein Macromolecules Utilizing 193nm Ultraviolet Photodissociation by : Michael B. Cammarata
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.
Book Synopsis The Encyclopedia of Mass Spectrometry: Hyphenated methods by : Michael L. Gross
Download or read book The Encyclopedia of Mass Spectrometry: Hyphenated methods written by Michael L. Gross and published by . This book was released on 2003 with total page 1092 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Enhancing the Characterization of Intact Proteins by Ultraviolet Photodissociation Mass Spectrometry by : Sean Duncan Dunham
Download or read book Enhancing the Characterization of Intact Proteins by Ultraviolet Photodissociation Mass Spectrometry written by Sean Duncan Dunham and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Access to high resolution mass spectrometers and high energy modes of activation such as electron- and photon-based modalities have enabled wider adoption of top-down methodologies, or strategies that allow the study of intact proteins. However, interpretation of MS/MS spectra of large proteins remains difficult owing to spectral congestion, charge capacity limitations, and other challenges. In particular, for ultraviolet photodissociation (UVPD) of intact proteins, a single laser pulse is typically used to avoid secondary dissociation of fragment ions that occurs when multiple pulses are employed. Consequently, a large amount of the precursor ion population remains undissociated, meaning a large portion of the potential signal is not effectively utilized. Secondary dissociation results in the generation of less informative small terminal and internal fragment ions. Internal fragments are typically ignored due to the computational challenges associated with accounting for them. The following research focuses on the use of fragment ion protection (FIP) during 193 nm UVPD to counter secondary dissociation when utilizing multiple laser pulses and the exploration of the benefits and pitfalls when considering internal fragment ions generated by 193 nm UVPD. In, summary, FIP increased the center sequence coverage of large proteins, but there is room for improvement. The inclusion of internal fragment ions can aid in enhancing the sequence coverage of intact proteins. However, the majority of internal fragment ions are not reliably identified across multiple replicates, reflecting a high risk of false positive identifications when they are considered. These findings are described in this thesis
Book Synopsis Mass Spectrometry-based Structural Proteomics by : Hao Zhang
Download or read book Mass Spectrometry-based Structural Proteomics written by Hao Zhang and published by . This book was released on 2011 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Converting gene-sequence information into functional information about a protein is a major challenge of post-genomic biology. Proteins have a variety of functions from serving as catalysts to acting as structural components; all these functions are closely related to protein structure. The first step to understand protein function is often a structural study of that protein. Two major approaches, NMR spectroscopy and X-ray crystallography, can provide an atomic-level, 3D structural model of a protein. The applications of these high resolution approaches, however, are limited by protein size, conformational flexibility, and aggregation propensity. To obtain complementary structural information about proteins, a variety of approaches from traditional structural biology (e.g., circular dichroism, fluorescence spectroscopy) to new advances (e.g., computational prediction, protein footprinting) are required. Mass spectrometry (MS) has become an important tool for studying protein structure, dynamics, interactions, and function. In particular, detailed characterization of protein-ligand interactions is now possible, a critical step toward understanding biological function. Mass spectrometric analysis of protein structure can take two approaches. First, protein-ligand interactions can be probed by chemical labeling followed by MS analysis to determine the resulting mass shift (extent of labeling) and the location of the labeling. This approach in a titration format gives protein-ligand affinities. The labeling takes place in solution, where biochemistry occurs, and can be under physiological conditions, whereas the mass spectrometer is used for analysis typically by bottom-up proteomic strategies. In the other approach, protein assemblies can also be transferred directly into the gas phase and interrogated by MS to afford structural insights. One can view this is a top-down approach. The measurements refer to a gas-phase species, and that raises the question of whether the outcomes of the measurements have relevance to the structure and properties of proteins in solution or in a living system. Although there are differences in experimental format, results, and sensitivity between the two approaches of MS-based protein structural analysis, the similarity of those approaches must not be overlooked. All MS-based structural analyses rely heavily on the identification of peptides, purified protein species, or protein complexes. This analysis has been accelerated by the developments of MS instrumentation and methodology in protein analysis; the structural information provided by MS-based analysis is greatly facilitated by having a structural model of the protein. The integrated results from MS approaches, traditional structural biology approaches (e.g., NMR and X-ray), and computational modeling give more complete structural information of proteins than that from any one of the approaches alone. In the first part of thesis, we focus on the development and application of chemical-labeling methods (protein footprinting) in studies of protein conformation. In the second part, a combined top-down approach of native ESI and electron-capture dissociation (ECD) in FTICR MSis presented for structural studies of protein assemblies in the gas phase.
