Download or read book The Development and Application of Methods for the Large scale Identification and Quantification of Proteins Using Mass Spectrometry written by and published by . This book was released on 2015 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: The work described in this dissertation highlights the versatility of mass spectrometry-based proteomics, detailing the development and/or application of several diverse methods that enable, and improve upon, the large-scale identification and/or quantification of whole proteomes. A broad overview of mass spectrometry-based proteomics and the technological innovations that have driven the field forward are presented in Chapter 1. Chapter 2 outlines a method that utilizes NeuCode SILAC labeling and machine learning algorithms to enable product ion annotation within tandem mass spectra, facilitating the implementation of both automated database searching and de novo sequencing. Chapter 3 presents a strategy for performing multiplexed quantification in the context of data-independent acquisition. Chapter 4 describes the extension of QuantMode, a strategy that utilizes gas-phase purification to improve the quantitative accuracy of isobaric tag-based methods, to an ETD-enabled ion trap system. Chapter 5 outlines a method that improves the sampling depth of label-free experiments without the use of offline fractionation or the significant increase in analysis time. In Chapter 6, both label-free and isobaric tag-based strategies are employed to evaluate the localization and functionality of proteins, protein phosphorylation, and protein acetylation within the various tissues of the model legume Medicago truncatula.
Download or read book Improvements to the Identification and Quantification of Peptides and Proteins written by Christopher Michael Rose and published by . This book was released on 2014 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: The following chapters contain a plethora of proteomic techniques aimed at the improvement of methods for the identification and quantification of peptide and protein species. The genesis of mass spectrometry for the analysis of biological molecules and the advances that have resulted in the large-scale identification and quantification of proteins are detailed in Chapter 1. Chapter 2 discusses the application of quantitative proteomic techniques for the large-scale analysis of a biological system, Medicago truncatula. The third chapter discusses the implementation of an online algorithm to identify peptides in real time (InSeq), enabling alterations to the instrument method that increase the quantitative accuracy of measurements or aid in post translational modification localization. Chapters 4 to 6 outline advances to the implementation of electron transfer dissociation aimed at increasing the ability to identify protein (Chapter 4) or peptide (Chapters 5 and 6) species. The remainder of this thesis details the application of neutron encoded (NeuCode) mass labels to peptide identification without tandem MS (Chapter 7), top-down quantification of intact proteoforms (Chapter 8), labeling of mammals that enables multiplexed quantitative analysis of mammalian tissue after only 10 days of labeling time (Chapter 9), and targeted quantification of more than 1,000 peptides (Chapter 10). Conclusions and future directions relating to the content of this thesis are discussed in Chapter 11.
Download or read book Proteome Research Mass Spectrometry written by Peter James and published by Springer Science & Business Media. This book was released on 2000-10-26 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in large scale DNA sequencing technology have made it possible to sequence the entire genome of an organism. Attention is now turning to the analysis of the product of the genome, the proteome, which is the set of proteins being expressed by a cell. Mass spectrometry is the method of choice for the rapid large-scale identification of these proteomes and their modifications. This is the first book to extensively cover the applications of mass spectrometry to proteome research.
Download or read book Computational and Statistical Methods for Protein Quantification by Mass Spectrometry written by Ingvar Eidhammer and published by John Wiley & Sons. This book was released on 2012-12-10 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: The definitive introduction to data analysis in quantitative proteomics This book provides all the necessary knowledge about mass spectrometry based proteomics methods and computational and statistical approaches to pursue the planning, design and analysis of quantitative proteomics experiments. The author’s carefully constructed approach allows readers to easily make the transition into the field of quantitative proteomics. Through detailed descriptions of wet-lab methods, computational approaches and statistical tools, this book covers the full scope of a quantitative experiment, allowing readers to acquire new knowledge as well as acting as a useful reference work for more advanced readers. Computational and Statistical Methods for Protein Quantification by Mass Spectrometry: Introduces the use of mass spectrometry in protein quantification and how the bioinformatics challenges in this field can be solved using statistical methods and various software programs. Is illustrated by a large number of figures and examples as well as numerous exercises. Provides both clear and rigorous descriptions of methods and approaches. Is thoroughly indexed and cross-referenced, combining the strengths of a text book with the utility of a reference work. Features detailed discussions of both wet-lab approaches and statistical and computational methods. With clear and thorough descriptions of the various methods and approaches, this book is accessible to biologists, informaticians, and statisticians alike and is aimed at readers across the academic spectrum, from advanced undergraduate students to post doctorates entering the field.
Download or read book Principles and Applications of Clinical Mass Spectrometry written by Nader Rifai and published by Elsevier. This book was released on 2018-06-26 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: Principles and Applications of Clinical Mass Spectrometry: Small Molecules, Peptides, and Pathogens is a concise resource for quick implementation of mass spectrometry methods in clinical laboratory work. Focusing on the practical use of these techniques, the first half of the book covers principles of chromatographic separations, principles and types of mass spectrometers, and sample preparation for analysis; the second half outlines the main applications of this technology within clinical laboratory settings, including determination of small molecules and peptides, as well as pathogen identification. A thorough yet succinct guide to using mass spectrometry technology in the clinical laboratory, Principles and Applications of Clinical Mass Spectrometry: Small Molecules, Peptides, and Pathogens is an essential resource for chemists, pharmaceutical and biotech researchers, certain government agencies, and standardization groups. Provides concrete examples of the main applications of mass spectrometry technology Describes current capabilities of the LC- and MS-based analytical methods Details methods for successful analytical work in the field
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 2017-05-26 with total page 282 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 Neuroproteomics written by Oscar Alzate and published by CRC Press. This book was released on 2009-10-26 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we beg
Download or read book Characterization of Protein Therapeutics using Mass Spectrometry written by Guodong Chen and published by Springer Science & Business Media. This book was released on 2014-07-08 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Mass Spectrometry Developmental Approaches to Answer Biological Questions written by Gwenael Pottiez and published by Springer. This book was released on 2015-02-05 with total page 77 pages. Available in PDF, EPUB and Kindle. Book excerpt: The understanding of the events taking place in a cell, a biological fluid or in any biological system is the main goal of biology research. Many fields of research use different technology to assess those events. Mass spectrometry is one of those techniques and this undergoes constant evolution and adaptation to always enhance the accuracy of the information provided. Proteomics provides a large panel of data on protein identity and protein expression that were made possible by mass spectrometry. For several years now mass spectrometry has become central to performing proteomic research, however this powerful tool is under constant evolution to be more sensitive and more resolute. More importantly mass spectrometry became a field of research focusing on new applications. Indeed, the complexity in biological systems relies on the changes of expression of transcription of proteins but also on the post-translational modification of proteins, the structure of proteins and the interaction between proteins, amongst others. As of now, several investigations tried to improve the quantification of proteins by mass spectrometry, the determination of post-translational modifications, the protein-protein and protein-nucleic acids interaction or the proteins structures. This book is structured as follows: after a brief introduction of the usual and most popular applications for mass spectrometry in proteomics, the most recent research and developments in mass spectrometry-based methodologies will be explored.
Download or read book LC MS MS in Proteomics written by Pedro R. Cutillas and published by Humana Press. This book was released on 2010-08-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the development of new quantitative strategies and powerful bioinformatics tools to cope with the analysis of the large amounts of data generated in proteomics experiments, liquid chromatography with tandem mass spectrometry (LC-MS/MS) is making possible the analysis of proteins on a global scale, meaning that proteomics can now start competing with cDNA microarrays for the analysis of whole genomes. In LC-MS/MS in Proteomics: Methods and Applications, experts in the field provide protocols and up-to-date reviews of the applications of LC-MS/MS, with a particular focus on MS-based methods of protein and peptide quantification and the analysis of post-translational modifications. Beginning with overviews of the use of LC-M/MS in protein analysis, the book continues with topics such as protocols for the analysis of post-translational modifications, with particular focus on phosphorylation and glycosylation, popular techniques for quantitative proteomics, such as multiple reaction monitoring, metabolic labelling, and chemical tagging, biomarker discovery in biological fluids, as well as novel applications of LC-MS/MS. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective subjects, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, LC-MS/MS in Proteomics: Methods and Applications presents the techniques and concepts necessary in order to aid proteomic practitioners in the application of LC-MS/MS to essentially any biological problem.
Download or read book Development and Application of Accurate Mass Measurements for Large scale Protein Interaction and Proteome Studies written by Chad R. Weisbrod and published by . This book was released on 2013 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: Traditionally and most commonly, accurate mass measurement is utilized to restrict peptide candidate search space on the precursor level to impart greater specificity in large peptide sequence databases. While use of accurate mass measurement is effective for discovery based proteomics, here we present novel applications of accurate mass measurement in proteomics to make further use of this expensive (monetarily and in time) acquisition attribute. This work began with the coupling and testing of a hybrid dual cell linear ion trap mass spectrometer (Velos) to a 7T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. This combination provides high speed, efficient ion accumulation with the high resolution and mass accuracy of FTICR. Using this mass spectrometer (Velos-FT) and an LTQ-Orbitrap it was shown theoretically and empirically that high resolution product ion spectra alone can be utilized to detect and quantify peptides. A DIA acquisition and data processing pipeline called, FT-All Reaction Monitoring (FT-ARM), was designed to exploit this observation. Direct similarities of FT-ARM to targeted proteomics data allow for discovery and targeted proteomics to be conducted in a single pass with little to no assay development. A search algorithm developed to score and assess data acquired using this strategy enabled quantitation into the attomole range and enabled identification within a complex background matrix. Specificity of the peptide assignment is attributed to the requirement of the simultaneous observation of a minimum number of product ions from the target peptide at a required mass measurement accuracy. Real-time informatics analysis during mass spectrometry acquisition can serve to simplify post-acquisition analysis and more importantly, focus measurements on ions more likely to yield the desired information. Real-time informatics applied to engineered, cleavable cross-linkers allows known mass relationships to be used to direct subsequent experiments. Peptides released from cross-linked complexes can be directly targeted for MS3 acquisition to obtain sequence information within a single LC/MS/MS acquisition. This new mass spectrometry method called Real-time Analysis for Cross-linked peptide Technology (ReACT) has been developed to enable assignment of cross-linked peptides "on-the-fly". Using ReACT, 708 unique cross-linked (
Download or read book Mass Spectrometry of Proteins and Peptides written by John R. Chapman and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Ridgelets written by Emmanuel Jean Candes and published by . This book was released on 1998 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single hidden-layer feedforward neural networks have been proposed as an approach to bypass the curse of dimensionality and are now becoming widely applied to approximation or prediction in applied sciences. In that approach, one approximates a multivariate target function by a sum of ridge functions; this is similar to projection pursuit in the literature of statistics. This approach poses new and challenging questions both at a practical and theorectical level, ranging from the construction of neural networks to their efficiency and capability. The topic of this thesis is to show that ridgelets, a new set of functions, provide an elegant tool to answer some of these fundamental questions ...
Download or read book Proteome Informatics written by Conrad Bessant and published by Royal Society of Chemistry. This book was released on 2016-11-15 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of proteomics has developed rapidly over the past decade nurturing the need for a detailed introduction to the various informatics topics that underpin the main liquid chromatography tandem mass spectrometry (LC-MS/MS) protocols used for protein identification and quantitation. Proteins are a key component of any biological system, and monitoring proteins using LC-MS/MS proteomics is becoming commonplace in a wide range of biological research areas. However, many researchers treat proteomics software tools as a black box, drawing conclusions from the output of such tools without considering the nuances and limitations of the algorithms on which such software is based. This book seeks to address this situation by bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, so that users of proteomics data can be confident that they are using appropriate tools in suitable ways.
Download or read book Quantitative Proteomics by Mass Spectrometry written by Salvatore Sechi and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a compendium of cutting-edge protocols for quantitative proteomics, and presents the most significant methods used in the field today. The focus on mass spectrometry (MS) is integral. Attention is given to state-of-the-art techniques for the characterization of the phosphoproteome and tandem MS for detection of inborn errors of metabolism. This volume is an indispensable resource in the search for novel biomarkers.
Download or read book Proteomics for Drug Discovery written by Iulia M. Lazar and published by . This book was released on 2017 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reflects the drug development communitys interest in proteomics methods by providing researchers with the necessary knowledge for the implementation of a number of basic experimental and bioinformatics protocols in the drug discovery research laboratory. The focus of the collection is on select protocols and methodologies that address the analysis of post-translational modifications, targeted protein quantification, protein-protein, protein-lipid, or protein-ATP interactions, in silicolead identification, protein arrays, tissue and cell extract preparation, labeling, chemoproteomics, and drug efficacy assessment. Emphasis was placed not just on methods that describe large-scale protein analysis, but also on ones that are amenable to future implementation in a high-throughput format. Written in the highly successfulMethods in Molecular Biologyseries format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and authoritative, Proteomics for Drug Discovery: Methods and Protocolsaims to provide a deep knowledge of the fundamentals of disease biology as well the means that were developed for probing the complex biological milieu.
Download or read book Application and Development of Mass Spectrometry Technologies to Enable Biological Investigations written by Gary M. Wilson and published by . This book was released on 2020 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: The research described in this dissertation showcases the utility and versatility of mass spectrometry for biological investigations and presents avenues for its continued improvement. Background on mass spectrometry-based proteomics and ancillary fields is provided in Chapter 1. Each subsequent chapter also includes a focused introduction to its respective contents. Chapters 2-4 were carried out in collaboration with members of the UW-Madison research community. We performed the proteomic sample preparation, analytical analysis, and data interpretation to advance the biological investigation. The manuscripts selected for these chapters highlight different proteomic techniques. The value of offline fractionation to increase analytical depth is presented in Chapter 2 to identify and quantify the protein regulators of zinc homeostasis during red blood cell development. In Chapter 3, global phosphoproteomics with tandem mass tags (TMT) is used to identify the role of an orphaned mitochondrial protein, Pptc7, and its importance in protein transport into mitochondria. The technique of transcriptomics-informed proteomics (proteogenomics) is featured in Chapter 4, in which novel proteins were identified in the lesser-studied life cycle of Toxoplasma gondii. Subsequent chapters delve into the enabling technologies developed \textit{en route} towards a robust, quantitative glycoproteomic pipeline. The study of the plasma glycoproteome in Chapter 5 highlights the benefits of using orthogonal enrichment methods and the optimization of MS parameters for intact glycopeptide profiling. Similarly, the design of a software environment, coined GlycoTools, to organize, inspect, and explore glycoproteomic data, with an emphasis on quality control, is presented in Chapter 6. Lastly, a large-scale glycoproteomic comparison of cell lines transformed with 6 different driving proliferative oncogenes is presented in Chapter 7, which was enabled by the concepts presented in Chapters 5 and 6.
