Download or read book Competitive Fragmentation Modeling of Mass Spectra for Metabolite Identification written by Felicity R. Allen and published by . This book was released on 2016 with total page 109 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the key obstacles to the effective use of mass spectrometry (MS) in high throughput metabolomics is the difficulty in interpreting measured spectra to accurately and efficiently identify metabolites. Traditional methods for automated metabolite identification compare the target MS spectrum to spectra of known molecules in a reference database, ranking candidate molecules based on the closeness of the spectral match. However the limited coverage of available databases has led to interest in computational methods for generating accurate reference MS spectra from chemical structures. This is the target application for this work. My main research contribution is to propose a method for spectrum prediction, which we call Competitive Fragmentation Modeling (CFM). I demonstrate that this method works effectively for both electron ionization (EI)-MS and electrospray tandem MS (ESI-MS/MS). It uses a probabilistic generative model for the fragmentation processes occurring in a mass spectrometer, and a machine learning approach to learn parameters for this model from data. CFM has been used in both a spectrum prediction task (ie, predicting the mass spectrum from a chemical structure), and in a putative metabolite identification task (ranking possible structures for a target spectrum). In the spectrum prediction task, CFM showed improved performance when compared to a full enumeration of all peaks corresponding to all substructures of the molecule. In the metabolite identification task, CFM obtained substantially better rankings for the correct candidate than existing methods. As further validation, this method won the structure identification category of the international Critical Assessment of Small Molecule Identification (CASMI) 2014 competition. The method is also available for general use via a web interface.
Download or read book Mass Spectrometry written by Edmond de Hoffmann and published by Wiley. This book was released on 2001-10-10 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: Offers a complete overview of the principles, theories and key applications of modern mass spectrometry in this introductory textbook. Following on from the highly successful first edition, this edition is extensively updated including new techniques and applications. All instrumental aspects of mass spectrometry are clearly and concisely described; sources, analysers and detectors. * Revised and updated * Numerous examples and illustrations are combined with a series of exercises to help encourage student understanding * Includes biological applications, which have been significantly expanded and updated * Also includes coverage of ESI and MALDI
Download or read book Plant Metabolomics written by Kazuki Saito and published by Springer Science & Business Media. This book was released on 2006-06-29 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics – which deals with all metabolites of an organism – is a rapidly-emerging sector of post-genome research fields. It plays significant roles in a variety of fields from medicine to agriculture and holds a fundamental position in functional genomics studies and their application in plant biotechnology. This volume comprehensively covers plant metabolomics for the first time. The chapters offer cutting-edge information on analytical technology, bioinformatics and applications. They were all written by leading researchers who have been directly involved in plant metabolomics research throughout the world. Up-to-date information and future developments are described, thereby producing a volume which is a landmark of plant metabolomics research and a beneficial guideline to graduate students and researchers in academia, industry, and technology transfer organizations in all plant science fields.
Download or read book Interpretation of MS MS Mass Spectra of Drugs and Pesticides written by Wilfried M. A. Niessen and published by John Wiley & Sons. This book was released on 2017-01-03 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides comprehensive coverage of the interpretation of LC–MS–MS mass spectra of 1300 drugs and pesticides Provides a general discussion on the fragmentation of even-electron ions (protonated and deprotonated molecules) in both positive-ion and negative-ion modes This is the reference book for the interpretation of MS–MS mass spectra of small organic molecules Covers related therapeutic classes of compounds such as drugs for cardiovascular diseases, psychotropic compounds, drugs of abuse and designer drugs, antimicrobials, among many others Covers general fragmentation rule as well as specific fragmentation pathways for many chemical functional groups Gives an introduction to MS technology, mass spectral terminology, information contained in mass spectra, and to the identification strategies used for different types of unknowns
Download or read book Inference in Hidden Markov Models written by Olivier Cappé and published by Springer Science & Business Media. This book was released on 2006-04-12 with total page 656 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a comprehensive treatment of inference for hidden Markov models, including both algorithms and statistical theory. Topics range from filtering and smoothing of the hidden Markov chain to parameter estimation, Bayesian methods and estimation of the number of states. In a unified way the book covers both models with finite state spaces and models with continuous state spaces (also called state-space models) requiring approximate simulation-based algorithms that are also described in detail. Many examples illustrate the algorithms and theory. This book builds on recent developments to present a self-contained view.
Download or read book Metabolomics Data Processing and Data Analysis Current Best Practices written by Justin Van Der Hooft and published by Mdpi AG. This book was released on 2021-09-10 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics data analysis strategies are central to transforming raw metabolomics data files into meaningful biochemical interpretations that answer biological questions or generate novel hypotheses. This book contains a variety of papers from a Special Issue around the theme "Best Practices in Metabolomics Data Analysis". Reviews and strategies for the whole metabolomics pipeline are included, whereas key areas such as metabolite annotation and identification, compound and spectral databases and repositories, and statistical analysis are highlighted in various papers. Altogether, this book contains valuable information for researchers just starting in their metabolomics career as well as those that are more experienced and look for additional knowledge and best practice to complement key parts of their metabolomics workflows.
Download or read book Statistical Analysis of Proteomics Metabolomics and Lipidomics Data Using Mass Spectrometry written by Susmita Datta and published by Springer. This book was released on 2016-12-15 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass spectrometry, time-of-flight data, and Fourier transform mass spectrometry are but a selection of the measurement platforms available to the modern analyst. Thus in practical proteomics or metabolomics, researchers will not only be confronted with new high dimensional data types—as opposed to the familiar data structures in more classical genomics—but also with great variation between distinct types of mass spectral measurements derived from different platforms, which may complicate analyses, comparison, and interpretation of results.
Download or read book Methodologies for Metabolomics written by Norbert W. Lutz and published by Cambridge University Press. This book was released on 2013-01-21 with total page 641 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics, the global characterisation of the small molecule complement involved in metabolism, has evolved into a powerful suite of approaches for understanding the global physiological and pathological processes occurring in biological organisms. The diversity of metabolites, the wide range of metabolic pathways and their divergent biological contexts require a range of methodological strategies and techniques. Methodologies for Metabolomics provides a comprehensive description of the newest methodological approaches in metabolomic research. The most important technologies used to identify and quantify metabolites, including nuclear magnetic resonance and mass spectrometry, are highlighted. The integration of these techniques with classical biological methods is also addressed. Furthermore, the book presents statistical and chemometric methods for evaluation of the resultant data. The broad spectrum of topics includes a vast variety of organisms, samples and diseases, ranging from in vivo metabolomics in humans and animals to in vitro analysis of tissue samples, cultured cells and biofluids.
Download or read book Mass Spectrometry Based Metabolomics written by Sastia Prama Putri and published by CRC Press. This book was released on 2016-04-21 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass Spectrometry-Based Metabolomics: A Practical Guide is a simple, step-by-step reference for profiling metabolites in a target organism. It discusses optimization of sample preparation for urine, serum, blood, tissue, food, and plant and animal cell samples. Encompassing three different technical fields-biology, analytical chemistry, and informa
Download or read book Interpretation of Mass Spectra written by Fred Warren McLafferty (Chemiker, USA) and published by . This book was released on 1973 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Increased Confidence of Metabolite Identification in High resolution Mass Spectra Using Prior Biological and Chemical Knowledge based Approaches written by Ralf Johannes Maria Weber and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry-based metabolomics aims to study endogenous, low molecular weight metabolites and can be used to examine a variety of biological systems. To substantially increase the accuracy of metabolite identification and increase coverage of the metabolome detected by high-resolution (HR) mass spectrometry I developed, optimised and/or employed several analytical and bioinformatics methods. Biological samples contain thousands of metabolites that are related through specific substrate-product transformations. This prior biological knowledge together with a mass error surface, which represents the mass accuracy of peak differences within mass spectra, were employed to significantly reduce the false positive rate of metabolite identification. To maximise the sensitivity of the Thermo LTQ FT Ultra mass spectrometer, the existing direct-infusion SIM-stitching acquisition parameters (Southam et al., 2007) were reoptimised, yielding a ca. 3-fold increase in sensitivity. Finally, relative isotopic abundance measurements (RIA) using HR direct-infusion MS were characterised on the two most popular Fourier transform MS instruments (FT-ICR and Oribitrap) using the reoptimised SIM-stitching acquisition parameters. Several novel observations regarding RIA measurements were reported. Utilising these RIA characterisations within a putative metabolite identification pipeline increased the number of single true empirical formula assignments compared to using accurate mass alone. To conclude, analytical and bioinformatics methods developed in this thesis have successfully facilitated the putative identification of hundreds of metabolites in several metabolomics studies.
Download or read book Mass Spectrometry in Drug Metabolism and Disposition written by Mike S. Lee and published by John Wiley & Sons. This book was released on 2011-03-16 with total page 648 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines the background, industrial context, process, analytical methodology, and technology of metabolite identification. It emphasizes the applications of metabolite identification in drug research. While primarily a textbook, the book also functions as a comprehensive reference to those in the industry. The authors have worked closely together and combine complementary backgrounds to bring technical and cultural awareness to this very important endeavor while serving to address needs within academia and industry It also contains a variety of problem sets following specific sections in the text.
Download or read book Analyzing Biomolecular Interactions by Mass Spectrometry written by Jeroen Kool and published by John Wiley & Sons. This book was released on 2015-05-04 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph reviews all relevant technologies based on mass spectrometry that are used to study or screen biological interactions in general. Arranged in three parts, the text begins by reviewing techniques nowadays almost considered classical, such as affinity chromatography and ultrafiltration, as well as the latest techniques. The second part focusses on all MS-based methods for the study of interactions of proteins with all classes of biomolecules. Besides pull down-based approaches, this section also emphasizes the use of ion mobility MS, capture-compound approaches, chemical proteomics and interactomics. The third and final part discusses other important technologies frequently employed in interaction studies, such as biosensors and microarrays. For pharmaceutical, analytical, protein, environmental and biochemists, as well as those working in pharmaceutical and analytical laboratories.
Download or read book Mass Spectrometry in Drug Metabolism written by Frigerio and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 527 pages. Available in PDF, EPUB and Kindle. Book excerpt: When a dose of drug is administered, three main phases of drug action may be distingushed. In the "pharmaceutical" phase the dosage form disintegrates, the active substance dissolves and becomes available for absorption. The second phase ("pharmaco kinetic" phase) includes absorption, distribution, metabolism, and excretion. That fraction of the dose which finally reaches the circulation after absorption will be available for biological action in the third, or "pharmacodynamic" phase when the drug reaches the target tissues and a drug-receptor interaction takes place. The objectives in studies of drug metabolism are: (a) to identify the pathways by which drugs are transformed in the body; (b) to ascertain quantitatively the importance of each pathway and intermediate; (c) to identify and quantify endogenous constituents influenced by the drug or its metabolites which may interfere with common metabolic processes. Since metabolites usually differ from their precursors by only a single chemical group, the resulting metabolic pathways generally consist of a series of closely related compounds. Mass spectrometry is uniquely suited for the analysis of drugs and metabolites for several reasons: only a minimal amount of sample preparation is needed, closely related compounds can be analyzed in a single step, structures can often be deduced directly from the mass spectra without the need for pure reference spectra, and constituents can be quantified with relative ease even when present in fractional nanogram quantity.
Download or read book Applications of Artificial Intelligence for Organic Chemistry written by Robert K. Lindsay and published by McGraw-Hill Companies. This book was released on 1980 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Enhancing the Identification of Small Molecules Based on Tandem Mass Spectra and Combinatorial Fragmentation written by Christoph Karl Heinz Ruttkies and published by . This book was released on 2022* with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational mass spectrometry, Tandem mass spectrometry (MS/MS), Combinatorial fragmentation, Small molecules, Metabolomics, Structural elucidation, MetFrag.
Download or read book Dictionary of Natural Products Supplement 4 written by John Buckingham and published by CRC Press. This book was released on 1997-09-25 with total page 638 pages. Available in PDF, EPUB and Kindle. Book excerpt: A dictionary of natural products. This fourth supplementary volume includes new and updated entries. It should be of interest to natural product chemists and bioscientists. Also available as a substructure searchable CD-ROM.
