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.
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.
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.
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
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.
Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research. - Describes the use of biomarkers to reduce clinical errors in research - Includes techniques from a range of biomarker discoveries - Covers all steps involved in biomarker discovery, from study design to study execution
In the human body, there are millions of living microorganisms involved in protecting the body from invaders, helping digestion and regulating moods, but there are also harmful pathogens that cause infectious diseases. For instance, the coronavirus (COVID-19) has caused considerable loss of life since its outbreak. Comprehensive analysis and characterization of microbes is of significant importance to understand the function and role of microorganisms, and rapid detection and identification of unknown pathogens are essential in early diagnosis, treatment monitoring and personalized medicine. Mass spectrometry is a technique to ionize molecules and detect the mass-to-charge ratio of the generated ions. The technique is widely used in hospitals for pathogenic bacteria identification, as well as in environmental science and food science for biosafety control. This book summarizes the most recent development of mass spectrometry techniques in microbial analysis, including mass spectrometry-based microbial identification, bacterial antimicrobial resistance study, data mining algorithm development, omics for microbial research, applications in clinical diagnosis, environmental science and food science, and more. It will guide researchers in the field, and those who are about to enter the field, in the most appropriate methods to characterize microbes and enable their detection.
Glycoproteins are central to numerous cellular processes and are among the most structurally complex biomolecules in nature. This unique complexity stems from variability in complex oligosaccharides that are located throughout the protein, a feature that is profoundly important for regulating biomolecular interactions but also makes glycoproteins difficult to study. As such, glycoprotein analysis entails a range of techniques to bridge the knowledge gap between glycoprotein structure and biological function. This book serves as an authoritative guide to glycoprotein analysis, written by internationally recognised experts in the field and discussed in the context of real-world applications across the life sciences. It provides a wide-ranging assessment of the modern methods, from those used to characterise glycoprotein structure, to approaches proficient in uncovering the molecular mechanisms by which they function as well as those capable of measuring structural dynamics and macromolecular assembly. These methods differ to a large extent and include mass spectrometry, glycan/lectin arrays, nuclear magnetic resonance, infrared spectroscopy, scanning probe microscopy and high-performance liquid chromatography. Equally important are computational techniques, including molecular dynamics and bioinformatics, which are also covered and discussed in the wider context of glycoprotein analysis. Glycobiology is indeed a rapidly growing field and the development of advanced tools for glycoproteins analysis has been enabled by researchers from different backgrounds working to overcome long-standing analytical challenges and biological questions involving glycosylation. This book is intended to aid academic and professional researchers at various levels of their career to gain a deeper appreciation of cutting-edge methods in glycoprotein analysis and their applications in biomolecular research, biotherapeutic development, structural biology and biophysical chemistry.
Mass spectrometry is one of the most versatile analytical techniques due to the vast range of analytes that it can detect and quantify and, as such, for its contribution to a significant number of life science fields. The legal and forensics community has certainly benefited from this technique, which has been able to provide reliable evidence in court cases. Liquid Chromatography/Gas Chromatography–Mass Spectrometry (LC/GC–MS) still have a dominant role in the provision of forensic intelligence. However, in the past decade new and exciting MS-based techniques have emerged and are or have evolved to be at an operational deployment maturity, enabling either fast, ambient, non-destructive, or portable screening (or encompass all of these features). In this book, developments of LC–MS and GC–MS based techniques are covered with respect to operational practice and new applications, accompanied by other MS-based techniques that are increasing forensic opportunities and that operate on a variety of evidence types. Whilst the underpinning working principles of each relevant mass spectrometry technique are summarised, each chapter primarily focuses on its implementation in criminal investigation and court cases. In the last chapters, this book additionally covers emerging MS technologies that are at the beginning of their operational implementation journey as well as niche applications outside the fields of traditional forensic science but with a clear potential to impact future investigations (forensics beyond the courtroom). This book provides an up-to-date reference for the mass spectrometry-based tools that are currently available both as established and as emerging methods within forensic practice. It will help casework commissioning managers and forensic providers worldwide to make more informed decisions as to the forensic strategy and workflow when examining exhibits. It is also recommended to postgraduates and early career investigators with reference to the contribution that these techniques and methods could make if applied to classic forensic science practice.
This book gathers, in a single resource, knowledge about matrix-assisted laser desorption ionisation (MALDI) mass spectrometry imaging. It includes fundamentals in the MALDI ionisation process, different source geometries and capabilities, detection systems and the latest research and applications in the range of –omics area as well as other broader areas. Chapters will touch on dedicated sample preparation protocols specific for the class of compounds of interest, instrumentation used with strengths and current limitations, strategies for structural analysis and identification and applications. It will be a welcomed addition to the literature in this fast-moving field and provide a guide to new innovations and applications especially in metabolomics and proteomics. With contributions from leading experts, this book will be an authoritative guide to this method. Aimed at postgraduate and professional researchers, in academia and in the industrial market where it has direct application to clinical research. It will be a supporting volume for those just entering the field as well as experienced practitioners.
