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 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 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 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 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 Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.

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 Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins

Download or read book Plant Systems Biology written by Sacha Baginsky and published by Springer Science & Business Media. This book was released on 2007-06-25 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume aims to provide a timely view of the state-of-the-art in systems biology. The editors take the opportunity to define systems biology as they and the contributing authors see it, and this will lay the groundwork for future studies. The volume is well-suited to both students and researchers interested in the methods of systems biology. Although the focus is on plant systems biology, the proposed material could be suitably applied to any organism.

Download or read book Mass spectrometric Methods for Quantitative Proteomics and Post translational Modification Mapping written by Ievgen Motorykin and published by . This book was released on 2015 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: Signal transduction within and between cells is at the core of biological activity in all living systems. Signaling networks are required for regulating biological functions, including growth, development and survival. Deregulation of signaling cascades has been linked to chronic and acute diseases and disorders This thesis focuses on mass spectrometry as a high resolution and high mass accuracy technique for the detection and characterization of proteins in biological systems. The thesis presents applications of contemporary mass-spectrometric methods to identify proteins, determine changes in their expression levels, and characterize post-translational modifications, in an effort to study changes in cell signaling in response to stress or disease. Various sample preparation methods to successfully suit needs of different biological questions were developed and applied: (1) extraction of the proteome, (2) chemical tagging and enrichment of the ATPome, a sub proteome comprising nucleotide binding proteins in particularly ATP-binding proteins including kinases, and (3) metal affinity complexation and enrichment of phosphopeptides. We used the following hybrid mass analyzer configurations: a quadrupole time-of-flight (qToF) instrument with ion mobility, a linear ion trap hyphenated with a FT-ICR mass spectrometry (LTQ-FT) and a hybrid ion trap-orbitrap mass spectrometer (Orbitrap Elite). The bioinformatic analysis of the proteomics data required multiple combinations of software packages to sequence proteins, perform absolute and relative quantification, statistically analyze and visualize data. Chapter 3 describes the use of zebrafish (Danio rerio) as one of the few vertebrate models that similar to humans cannot synthesize vitamin C to investigate the system-wide consequences of deficiencies in two essential micronutrients, vitamins E and C, on the proteome biology. A label-free proteomics workflow was applied to detect changes in protein abundance estimates dependent on vitamin regimes. The study reveals suppression in an energy metabolism cycle, glycolysis, in vitamin C and E deficient zebrafish. It was discovered that alternative energy cycle, glutaminolysis, is activated to fulfill energy requirement. Chapter 4 focuses on the determination of proteome differences that can be linked to the propensity of metastasis in osteosarcoma (OS), a bone cancer that predominantly targets the adolescent age group. OS has a high propensity to metastasize to the lungs, which is associated with a poor prognosis. The study utilizes canine osteosarcoma cell lines that were originally obtained from orthotropic primary OS and metastatic cells. Canis familiaris, the domestic dog, is an established large animal model of OS that recapitulate many biological and clinical features of the human malignancy. We applied a two-prone comparative proteomics approach that consisted of: (a) determination of protein abundance levels and (b) focus on kinases, a functional sub-proteome, using a chemical affinity tag for enrichment of ATP-binding proteins. Findings of this study indicated that in the highly metastasizing canine osteosarcoma cell line proteins associated with extracellular adhesion were deregulated, which may enhance metastogenesis. Mitogen activated protein kinases MAP2K6, MAP4K3, MAP4K4, MAP4K5, ZAK and v-akt murine thymoma viral oncogene homolog 1, AKT1, are among those expressed in significantly lower abundance in the highly metastasizing canine osteosarcoma cell line indicating changes in cell signaling. Chapter 5 describes the development and application of a multiple protease protocol (Trypsin, LysC, AspN, Chymotrypsin and GluC) for improving the number of phosphosite identifications in a large-scale phosphoproteomics studies. The method combines immobilized titanium ion affinity chromatography (Ti4+-IMAC) with a data-dependent, decision tree-based data acquisition technique utilizing two complementary fragmentation methods, namely collision induced dissociation (CID) and electron transfer dissociation. The multiple protease protocol was applied to human leukemic T cell lymphoblasts (Jurkat E6.1) and resulted in the detection of >11,000 unique phosphosites, the most comprehensive identification among methods that use similar phosphopeptide enrichment approach.

Download or read book 2 D Proteome Analysis Protocols written by Andrew J. Link and published by Springer Science & Business Media. This book was released on 2008-02-02 with total page 585 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the completion of sequencing projects and the advancement of a- lytical tools for protein identification, proteomics—the study of the expressed part of the genome—has become a major region of the burgeoning field of functional genomics. High-resolution 2-D gels can reveal virtually all p- teins present in a cell or tissue at any given time, including posttranslationally modified proteins. Changes in the expression and structure of most cellular proteins caused by differentiation or external stimuli can be displayed and eventually identified using 2-D protein gels. 2-D Proteome Analysis Protocols covers all aspects of the use of 2-D protein electrophoresis for the analysis of biological problems. The contri- tors include many of the leaders in the fields of biochemistry and analytical chemistry who were instrumental in the development of high-resolution 2-D gels, immobilized pH gradients, computer analysis, and mass spectromet- based protein identification methodologies. This book is intended as a benchtop manual and guide both for novices to 2-D gels and for those aficionados who wish to try the newer techniques. Any group using protein biochemistry—especially in the fields of molecular biology, biochemistry, microbiology, and cell biology—should find this book eminently useful. 2-D Proteome Analysis Protocols takes the researcher through the c- plete process of working with 2-D protein gels from making the protein - tract to finally identifying the proteins of interest. It includes protocols for generating 2-D protein extracts from most of the standard model organisms, including bacteria, yeast, nematode, Drosophila, plants, mouse, and human.

Download or read book Mass Spectrometry of Proteins and Peptides written by Mary S. Lipton and published by Humana Press. This book was released on 2014-11-27 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: When the last edition of this book was published in 2000, the field of proteomics was in its infancy. At that time, multidimensional liquid chromatographic separations were being introduced as an alternative to traditional gel-based techniques for separating complex protein and peptide mixtures prior to mass spectrometric detection. Today, this approach – referred to as shotgun proteomics – is considered routine for lar- scale global analyses of protein mixtures. Now in its adolescence, proteomics is fundamentally transforming biological and medical research. Much of this transformation can be attributed to technological advancements, particularly in mass spectrometry. Much wider accessibility of hi- resolution and mass measurement accuracy instrumentation in recent years has ini- ated a new revolution in the field by providing more reliable data and shifting the focus from cataloging proteins to precisely quantifying changes in protein abundance over time and in response to stimuli. Advanced mass spectrometers and novel ion d- sociation schemes such as electron transfer/capture dissociation make it possible to venture boldly into the maze of protein posttranslational modifications, which are an integral component of understanding functional proteomics in the spatial and t- poral domains. Another area that has benefited from these advancements is top-down proteomics, an emerging method essential for characterizing various protein variants that has potentially high impact in biomedical research.

Download or read book Handbook of Research on Systems Biology Applications in Medicine written by Daskalaki, Andriani and published by IGI Global. This book was released on 2008-11-30 with total page 982 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book highlights the use of systems approaches including genomic, cellular, proteomic, metabolomic, bioinformatics, molecular, and biochemical, to address fundamental questions in complex diseases like cancer diabetes but also in ageing"--Provided by publisher.

Download or read book Selected Reaction Monitoring Mass Spectrometry SRM MS in Proteomics written by Mahmud Hossain and published by Springer Nature. This book was released on 2020-09-26 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering a wide-ranging facet of a “gold-standard” targeted mass spectrometry (MS) method for the consistent detection and accurate quantification of preselected proteins in complex biological matrices, Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics: A Comprehensive View describes: The knowledge-based development of highly efficient SRM methodology including assay workflow, selection of proteins, peptides, transitions and its validation, and quality assessment Available bioinformatic tools – for both pre-acquisition method development and post-MS acquisition data analysis and data repositories Various relative and absolute quantification techniques SRM-MS’ widespread applications in biomarker development and in clinical studies, as well as in the analysis of various posttranslational modifications (PTMs) Current challenges and contemporary trends to overcome those difficulties In addition, it features the historical development of modern-day mass spectrometry with its vivid applications and also covers basic MS instrumentation, ionization techniques, and various proteomics approaches. Comprehensive discussion, extensive references at the end of each chapter, and the list of review articles in the bibliography offer invaluable resources for advanced readings. Researchers from the undergraduate to postgraduate level and beyond in both academic or industry settings studying and working on mass spectrometry and/or proteomics will benefit from this book.

Download or read book Plant Proteomics written by Jozef Samaj and published by Springer Science & Business Media. This book was released on 2007-09-09 with total page 397 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant Proteomics highlights rapid progress in this field, with emphasis on recent work in model plant species, sub-cellular organelles, and specific aspects of the plant life cycle such as signaling, reproduction and stress physiology. Several chapters present a detailed look at diverse integrated approaches, including advanced proteomic techniques combined with functional genomics, bioinformatics, metabolomics and molecular cell biology, making this book a valuable resource for a broad spectrum of readers.

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 Salmonella written by Bassam Annous and published by BoD – Books on Demand. This book was released on 2012-07-18 with total page 519 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discovery of Salmonella in swine in 1885 marked the beginning of intense efforts to control salmonellae that have continued for the past 127 years. The majority of foodborne outbreaks are caused by only a few of the 2500+ known serovars. While progress has been made on many fronts, salmonellosis has yet to be eliminated in either developed or in developing nations. This work represents the collective contributions of authors from all around the world. Chapters in this book address a wide array of topics related to understanding and controlling this pathogen, including: Salmonella as studied in the environment, air and in food products; virulence and pathogenicity; control by bacteriophages and other antimicrobials; bacterial adaptation; etc.