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Processing Metabolomics and Proteomics Data with Open Software

Processing Metabolomics and Proteomics Data with Open Software
Author: Robert Winkler
Publisher: Royal Society of Chemistry
Total Pages: 460
Release: 2020-03-19
Genre: Science
ISBN: 1788017218
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Metabolomics and proteomics allow deep insights into the chemistry and physiology of biological systems. This book expounds open-source programs, platforms and programming tools for analysing metabolomics and proteomics mass spectrometry data. In contrast to commercial software, open-source software is created by the academic community, which facilitates the direct interaction between users and developers and accelerates the implementation of new concepts and ideas. The first section of the book covers the basics of mass spectrometry, experimental strategies, data operations, the open-source philosophy, metabolomics, proteomics and statistics/ data mining. In the second section, active programmers and users describe available software packages. Included tutorials, datasets and code examples can be used for training and for building custom workflows. Finally, every reader is invited to participate in the open science movement.

Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry

Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry
Author: Susmita Datta
Publisher: Springer
Total Pages: 295
Release: 2016-12-15
Genre: Medical
ISBN: 3319458094
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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.

Mass Spectrometry in Food Analysis

Mass Spectrometry in Food Analysis
Author: Leo M. L. Nollet
Publisher: CRC Press
Total Pages: 462
Release: 2022-03-21
Genre: Technology & Engineering
ISBN: 1000539253
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The quality and safety of food are crucial for human nutrition. However, evaluating the chemical composition of food is challenging for the analyst and requires powerful methods. Chromatography and mass spectrometry (MS) is the gold standard for analyzing complex food samples, including raw materials and intermediate and finished products. Mass Spectrometry in Food Analysis covers the MS-based analysis of different aspects of food quality, which include nutritional value, profile of macronutrients (proteins, lipids, and carbohydrates), micronutrients (vitamins), and nutraceutical active compounds. Additionally, sensory quality, flavor, food pigments, safety, and detection of pesticides, contact materials, veterinary drugs and pharmaceuticals, organic pollutants, and pathogens are covered. Key Features: Contains the basics of mass spectrometry and experimental strategies Explores determination of macro- and micronutrients Analyzes sensory and nutraceutical food quality Discusses detection of contaminants and proof of authenticity Presents emerging methods for food analysis This book contains an introductory section that explains the basics of MS and the difference between targeted and untargeted strategies for beginners. Further, it points out new analytical challenges, such as monitoring contaminants of emerging concern, and presents innovative techniques (e.g., ambient ionization MS and data mining). Also available in the Food Analysis & Properties Series: Nanoemulsions in Food Technology: Development, Characterization, and Applications, edited by Javed Ahmad and Leo M.L. Nollet (ISBN: 978-0-367-61492-8) Sequencing Technologies in Microbial Food Safety and Quality, edited by Devarajan Thangadurai, Leo M.L. Nollet, Saher Islam, and Jeyabalan Sangeetha (ISBN: 978-0-367-35118-2) Chiral Organic Pollutants: Monitoring and Characterization in Food and the Environment, edited by Edmond Sanganyado, Basil K. Munjanja, and Leo M.L. Nollet (ISBN: 978-0-367-42923-2) For a complete list of books in this series, please visit our website at: www.crcpress.com/Food-Analysis--Properties/book-series/CRCFOODANPRO

Advanced Mass Spectrometry-based Analytical Separation Techniques for Probing the Polar Metabolome

Advanced Mass Spectrometry-based Analytical Separation Techniques for Probing the Polar Metabolome
Author: Rawi Ramautar
Publisher: Royal Society of Chemistry
Total Pages: 367
Release: 2021-07-13
Genre: Science
ISBN: 1839163534
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The efficient analysis of polar and charged metabolites in biological samples remains a huge challenge in the field of metabolomics. Over the past years, novel mass spectrometry-based analytical tools have been developed to enable the sensitive and efficient profiling of polar ionogenic metabolites in various biological samples. This book gives the reader a comprehensive overview of these recent technological developments. Topics covered include the use of chemical labelling strategies for allowing the analysis of polar metabolites using reversed-phase liquid chromatography–mass spectrometry (RPLC-MS) and the latest methodological developments in RPLC-MS, hydrophilic interaction liquid chromatography (HILIC)-MS and ion-pair LC-MS approaches. Attention is also paid to developments in nano-LC-MS and capillary electrophoresis–mass spectrometry methods specifically for profiling polar metabolites in small volume biological samples. The utility of ion-mobility MS and NMR spectroscopy will also be outlined. Sample preparation is the key part in the analytical workflow employed for metabolomics. Therefore, ample emphasis will be given on recent solid-phase extraction and solid-phase micro-extraction methods. Finally, analytical techniques for chiral metabolic profiling will also be considered. Discussing the state-of-the-art of the proposed topics in one single book for probing the polar metabolome, using relevant examples, is unique and needed in the metabolomics field. This book has relevance and appeal to an international audience of analytical and biomedical researchers in industry and academia.

MALDI Mass Spectrometry Imaging

MALDI Mass Spectrometry Imaging
Author: Tiffany Siegel Porta
Publisher: Royal Society of Chemistry
Total Pages: 541
Release: 2021-12-03
Genre: Science
ISBN: 1839162414
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This book gathers knowledge about matrix-assisted laser desorption ionisation (MALDI) mass spectrometry imaging for postgraduate and professional researchers in academia and in industry where it has direct application to clinical research.

Ion Mobility-Mass Spectrometry

Ion Mobility-Mass Spectrometry
Author: Alison E Ashcroft
Publisher: Royal Society of Chemistry
Total Pages: 547
Release: 2021-11-11
Genre: Science
ISBN: 1839162899
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Over the last decade, the use of ion mobility separation in combination with mass spectrometry analysis has developed significantly. This technique adds a unique extra dimension enabling the in-depth analysis of a wide range of complex samples in the areas of the chemical and biological sciences. Providing a comprehensive guide to the technique, each chapter is written by an internationally recognised expert and with numerous different commercial platforms to choose from, this book will help the end users understand the practicalities of using different instruments for different ion mobility purposes. The first section provides a detailed account of the fundamentals behind the technique and the current range of available instrumentation. The second section focusses on the wide range of applications that have benefitted from ion mobility – mass spectrometry and includes topics taken from current research in the pharmaceutical, metabolomics, glycomics, and structural molecular biology fields. The book is primarily aimed at researchers, appealing to practising chemists and biochemists, as well as those in the pharmaceutical and medical fields.

Advanced Fragmentation Methods in Biomolecular Mass Spectrometry

Advanced Fragmentation Methods in Biomolecular Mass Spectrometry
Author: Frederik Lermyte
Publisher: Royal Society of Chemistry
Total Pages: 359
Release: 2020-12-11
Genre: Science
ISBN: 1839161108
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Breaking down large biomolecules into fragments in a controlled manner is key to modern biomolecular mass spectrometry. This book is a high-level introduction, as well as a reference work for experienced users, to ECD, ETD, EDD, NETD, UVPD, SID, and other advanced fragmentation methods. It provides a comprehensive overview of their history, mechanisms, instrumentation, and key applications. With contributions from leading experts, this book will act as an authoritative guide to these methods. Aimed at postgraduate and professional researchers, mainly in academia, but also in industry, it can be used as supplementary reading for advanced students on mass spectrometry or analytical (bio)chemistry courses.

Microbiome-Based Decontamination of Environmental Pollutants

Microbiome-Based Decontamination of Environmental Pollutants
Author: Ajay Kumar
Publisher: Elsevier
Total Pages: 495
Release: 2024-04-01
Genre: Science
ISBN: 0443217807
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Microbiome-Based Decontamination of Environmental Pollutants explores the complex interactions of plant-associated microbiomes, providing insights into the pressing challenges of managing environmental resources such as soil, water, and waste. Analysis has shown a formidable potential based in the network interactions between plant microbiota and environmental contaminants. This book presents insights into the potential exploitation of these plant-associated microbial functions. This volume in the Plant and Soil Microbiome series summarizes microbiological aspects of environmental management from the basics to advanced theoretical as well as practical aspects of microbial-based approaches. The physical and chemical changes caused by pollution of an ecosystem can occur rapidly, significantly impacting the functionality of ecosystem services in that environment. Environmental contamination poses and increasingly global challenge through direct and indirect adverse impacts on the climate, soil productivity and the health concerns of human beings. Traditional remediation techniques are not consistently feasible in mitigating environmental contaminants challenges in terms of cost-effectiveness, limited land resources and toxic residual products. The use of plant-associated microbes as part of a network of tools opens a new door to explore an alternative, eco-friendly and economical technology to mitigate the challenges of environmental contamination. Explores the emerging plant microbe interactive nexus for contaminants degradation Presents insights into the production and commercialization of plant-microbiome based enzymes Includes engineered microbes and microbial products application in contaminant management Highlights the latest omics and technologies used in plant–soil microbiome in contaminant management