The Development of Novel MALDI and Nanoelectrospray Mass Spectrometry Methods for the Improved Analysis of Proteins and Peptides PDF Download
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Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 233
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Book Description
The development of matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) gave rise to the era of biological mass spectrometry and the new field of proteomics. Two recurring problems that are central to advancing the science of proteomics are the development of reliable mass spectrometry methods to identify proteins and to sequence peptides. The specificity of proteases such as trypsin in combination with the high mass accuracy provided by reflectron time-of-flight mass analyzers, allows the reliable identification of a protein from the mass spectrum of its proteolytic digestion products in an experiment known as peptide mass fingerprinting. Some powerful approaches to improve the confidence of the identification of proteins in the peptide mass fingerprinting experiment have been described in this dissertation. Both approaches described in this dissertation involve the optimization of different aspects of the sample preparation step in the MALDI-TOF mass spectrometry experiment. Precursor-ion scanning in the negative ion mode followed by sequencing in the positive ion mode is a powerful strategy employed to identify and sequence phosphopeptides via nanoelectrospray triple quadrupole mass spectrometry. Less sample and time would be consumed if both of the aforementioned steps could be carried out in the negative ion mode. Nanoelectrospray tandem mass spectrometry in the negative ion mode is usually not successful as traditional gold-coated emitters undergo electrical discharge. Using polyaniline-coated emitters, we have demonstrated that peptides can be sequenced successfully in the negative-ion mode enabling the observation of a wealth of information that is not available in the corresponding positive-ion mode experiment.
Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 233
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Book Description
The development of matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) gave rise to the era of biological mass spectrometry and the new field of proteomics. Two recurring problems that are central to advancing the science of proteomics are the development of reliable mass spectrometry methods to identify proteins and to sequence peptides. The specificity of proteases such as trypsin in combination with the high mass accuracy provided by reflectron time-of-flight mass analyzers, allows the reliable identification of a protein from the mass spectrum of its proteolytic digestion products in an experiment known as peptide mass fingerprinting. Some powerful approaches to improve the confidence of the identification of proteins in the peptide mass fingerprinting experiment have been described in this dissertation. Both approaches described in this dissertation involve the optimization of different aspects of the sample preparation step in the MALDI-TOF mass spectrometry experiment. Precursor-ion scanning in the negative ion mode followed by sequencing in the positive ion mode is a powerful strategy employed to identify and sequence phosphopeptides via nanoelectrospray triple quadrupole mass spectrometry. Less sample and time would be consumed if both of the aforementioned steps could be carried out in the negative ion mode. Nanoelectrospray tandem mass spectrometry in the negative ion mode is usually not successful as traditional gold-coated emitters undergo electrical discharge. Using polyaniline-coated emitters, we have demonstrated that peptides can be sequenced successfully in the negative-ion mode enabling the observation of a wealth of information that is not available in the corresponding positive-ion mode experiment.
Author: John R. Chapman
Publisher: Springer Science & Business Media
ISBN: 1592590454
Category : Science
Languages : en
Pages : 539
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Book Description
Little more than three years down the line and I am already writing the Preface to a second volume to follow Protein and Peptide Analysis by Mass . What has happened in between these times to make this second venture worthwhile? New types of mass spectrometric instrumentation have appeared so that new techniques have become possible and existing techniques have become much more feasible. More particularly, however, the newer ionization te- niques, introduced for the analysis of high molecular weight materials, have now been thoroughly used and studied. As a result, there has been an en- mous improvement in the associated sample handling technology so that these methods are now routinely applied to much smaller sample amounts as well as to more intractable samples. Again, this particular community of mass spectrometry users has both increased in number and diversified. And, riding this wave of acceptance, leaders in the field have set their sights on more complex problems: molecular interaction, ion structures, quantitation, and kinetics are just a few of the newer areas reported in Mass Spectrometry of Proteins and Peptides. As with the first volume, one purpose of this collection, Mass Spectr- etry of Proteins and Peptides, is to show the reader what can be done by the application of mass spectrometry, and perhaps even to encourage the reader to venture down new paths.
Author: Oscar Alzate
Publisher: CRC Press
ISBN: 1420076264
Category : Medical
Languages : en
Pages : 356
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Book Description
In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we beg
Author: Richard B. Cole
Publisher: John Wiley & Sons
ISBN: 1118211553
Category : Science
Languages : en
Pages : 900
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Book Description
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.
Author: Hua Xu
Publisher:
ISBN:
Category : Bioinformatics
Languages : en
Pages :
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Book Description
Abstract: Tandem mass spectrometry is one of the most important tools for protein analysis. This thesis is focused on the development of new methods and algorithms for tandem mass spectrometry data analysis. A database search engine, MassMatrix, has also been developed that incorporates these methods and algorithms. The program is publicly available both on the web server at www.massmatrix.net and as a deliverable software package for personal computers. Three different scoring algorithms have been developed to identify and characterize proteins and peptides by use of tandem mass spectrometry data. The first one is targeted at the next generation of tandem mass spectrometers that are capable of high mass accuracy and resolution. Two scores calculated by the algorithm are sensitive to high mass accuracy due to the fact that this new algorithm explicitly incorporates mass accuracy into scoring potential peptide and protein matches for tandem mass spectra. The algorithm is further improved by employing Monte Carlo Simulations to calculate ion abundance based scores without any assumptions or simplifications. For high mass accuracy data, MassMatrix provides improvements in sensitivity over other database search programs. The second scoring algorithm based on peptide sequence tags inferred from tandem mass spectra further improves the performance of MassMatrix for low mass accuracy tandem mass spectrometry data. The third algorithm is the first automated data analysis method that uses peptide retention times in liquid chromatography to evaluate potential peptide matches for tandem mass spectrometry data. The algorithm predicts reverse phase liquid chromatography retention times of peptides by their hydrophobicities and compares the predicted retention times with the observed ones to evaluate the peptide matches. In order to handle low quality data, a new method has also been developed to reduce noise in tandem mass spectra and screen poor quality spectra. In addition, a data analysis method for identification of disulfide bonds in proteins and peptides by tandem mass spectrometry data has been developed and incorporated in MassMatrix. By this new approach, proteins and peptides with disulfide bonds can be directly identified in tandem mass spectrometry with high confidence without any chemical reduction and/or other derivatization.
Author: Willy Vincent Bienvenut
Publisher: Springer Science & Business Media
ISBN: 9781402033186
Category : Medical
Languages : en
Pages : 324
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Book Description
At present where protein identification and characterisation using mass spectrometry is a method of choice, this book is presenting a review of basic proteomic techniques. The second part of the book is related to the novel high throughput protein identification technique called the 'molecular scanner'. Several protein identification techniques are described, especially the peptide mass fingerprint with MALDI-MS based method. E.g. ionisation process, matrix available, signal reproducibility and suppression effect, as well as date treatment for protein identification using bioinformatics tools.
Author: Matthew Rush
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
The work described in this dissertation involves the development and application of mass spectrometry methods for the analysis of peptides, proteins, and metabolites. Chapter 1 gives a brief overview of the history and fundamentals of bioanalytical mass spectrometry, the utility of electron transfer dissociation (ETD) for the analysis of peptides and proteins, and the use of high resolution gas-chromatography mass spectrometry (GC-MS) to characterize volatile small molecule metabolites from complex mixtures. Chapter 2 explores the role of the reagent cation in negative electron transfer dissociation (NETD) for the analysis of peptide anions. Then Chapter 3 demonstrates the use of activated-ion NETD (AI-NETD) to analyze the negative-mode proteome of yeast. This work proved to generate far greater depth of coverage than previous negative-mode experiments, owing largely to the introduction of IR radiation concurrent to the NETD reaction, which proved to drastically improve peptide identification. For this study, a high pH chromatography method was also developed to greatly improve the ionization of peptide anions using negative electrospray ionization. Chapter 4 characterizes activated-ion ETD (AI-ETD) as a fragmentation method to interrogate proteins with intact disulfide bonds. This method greatly improved the sequence coverage and sequence ion generation compared to other commonly used fragmentation techniques for a set standard proteins. Chapter 5 outlines the creation of a high resolution metabolite mass spectral library using a Q Exactive GC mass spectrometer. This library is then employed to identify metabolites from yeast and human cell cultures, significantly improving the identification confidence over commercially available spectral libraries. Lastly, Chapter 6 describes the multi-omic analysis of yeast strains with a single gene deletion, aiming to correlate genes of known function with genes unknown function.
Author: Guodong Chen
Publisher: Springer Science & Business Media
ISBN: 1441978623
Category : Science
Languages : en
Pages : 408
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Book Description
This book highlights current approaches and future trends in the use of mass spectrometry to characterize protein therapies. As one of the most frequently utilized analytical techniques in pharmaceutical research and development, mass spectrometry has been widely used in the characterization of protein therapeutics due to its analytical sensitivity, selectivity, and specificity. This book begins with an overview of mass spectrometry techniques as related to the analysis of protein therapeutics, structural identification strategies, quantitative approaches, followed by studies involving characterization of process related protein drug impurities/degradants, metabolites, higher order structures of protein therapeutics. Both general practitioners in pharmaceutical research and specialists in analytical sciences will benefit from this book that details step-by-step approaches and new strategies to solve challenging problems related to protein therapeutics research and development.
Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 768
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Book Description
Author: Mike S. Lee
Publisher: John Wiley & Sons
ISBN: 1118605195
Category : Science
Languages : en
Pages : 290
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Book Description
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
