New Developments in Mass Spectrometry – serie

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.

Capillary electrophoresis–mass spectrometry (CE-MS) has become a very useful analytical technique for the profiling of highly polar and charged metabolites in biological samples. In this book, the unique features of CE-MS for metabolomics studies are highlighted including CE separation modes, capillary coatings and practical aspects of CE-MS coupling alongside a comprehensive overview of recent technological developments and applications. CE-MS can be considered a relatively new technique in the field of metabolomics and it is therefore important to inform the scientific community about the possibilities of advanced CE-MS approaches for metabolomics studies. This book outlines the potential of this technique for researchers working in metabolomics, bioanalytics and biomarker analysis.

Lipidomics is one of the emerging ‘omics’ techniques with growing importance in bioscience. Discussing interesting standard and non-standard techniques relevant to the measurement and analysis of lipids by mass spectrometry, this book will provide a guide to the possibilities of the techniques. It will introduce the reader to exciting new methods that allow isomer differentiation, improve sensitivity, allow spatial location and go beyond annotation of simply matching a mass to a database entry. The book is written and edited by the some of the world leaders in the field of lipid mass spectrometry and will have international appeal in industry and academia for analytical chemists, biochemists and biotechnologists. Furthermore, it will provide a useful resource for anyone interested in lipid structure characterization particularly for graduates and postgraduates who require a starting point for their projects.

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.

Secondary ion mass spectrometry (SIMS) is a technique used to analyse the composition of solid surfaces and thin films by sputtering the surface of the specimen with a primary ion beam and collecting and analysing ejected secondary ions. The technique has been applied to quality assurance in semiconductor manufacture, in forensics for enhancement of fingerprints and to determine the composition of cometary dust. This book briefly introduces the fundamentals of the SIMS technique and discusses in detail recent advancements and applications in various branches of science. From an extensive literature review, it provides a good overview of how to reproduce the most prominent experiments and what instruments are required or suited to the analysis. It will inspire new designs and hence research for the future. Appealing to graduates or postgraduates who want an overview of the field and how to use this technique, researchers new to this field will find innovative solutions and how to achieve them detailed herein.

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.

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.

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.

This book gathers, in a single resource, fundamental and applied 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 a range of –omics areas as well as other broader areas. Chapters touch on dedicated sample preparation protocols specific to 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 spatial metabolomics and proteomics, among others.With contributions from leading experts, this book is an authoritative guide to this method. It is aimed at postgraduate and professional researchers in academia and in the industrial market, where it has direct application to (pre) clinical research. It will be a supporting volume for those just entering the field as well as experienced practitioners.

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.

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.

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 was triggered by the success story of sector field mass spectrometry in elemental and isotopic analysis since the first presentation of the mass spectrum of Ne a hundred years ago. The outstanding and unique features of sector field mass spectrometry - high sensitivity, high mass resolution and simultaneous multiple ion detection – have paved the way for its widespread and successful application across different scientific disciplines.　 Written, compiled and edited by world renowned experts, this book is intended to provide deep insight into the topic along with fundamental knowledge about elemental and isotopic analysis. Aimed at scientists in the field of natural and life sciences, instrument manufacturers, practitioners and graduate students, it provides solid information about the methodological background and analytical capabilities of sector field mass spectrometry. A detailed description of peculiarities and an overview of the most relevant applications making use of specific techniques employing sector field mass analysers (ICP-MS, GDMS, TIMS, SIMS and IRMS) are given, including a presentation of the currently available commercial instruments. This approach guarantees that readers are thoroughly introduced to and familiarized with the fascinating inter- and transdisciplinary field of sector field mass spectrometry.

As a component of post-genome science, the field of proteomics has assumed great prominence in recent years. Whereas quantitative analyses focussed initially on relative quantification, a greater emphasis is now placed on absolute quantification and consideration of proteome dynamics. Coverage of the topic of quantitative proteomics requires consideration both of the analytical fundamentals of quantitative mass spectrometry and the specific demands of the problem being addressed.Quantitative Proteomics aims to outline the state of the art in mass spectrometry-based quantitative proteomics, describing recent advances and current limitations in the instrumentation used, together with the various methods employed for generating high quality data. Details on both strategies describing how stable isotope labelling can be applied and methods for performing quantitative analysis of proteins in a label-free manner are given. The utility of these strategies to understanding cellular protein dynamics are then exemplified with chapters looking at spatial proteomics, dynamics of protein function as determined by quantifying changes in protein post-translational modification and protein turnover. Finally, a key application of these techniques to biomarker discovery and validation is presented, together with the rapidly developing area of quantitative analysis of protein-based foodstuffs.This exemplary book is essential reading for analytical and biological mass spectrometrists working in proteomics research, as well as those undertaking either fundamental or clinical-based investigations with an interest in understanding protein dynamics and/or biomarker assessment.

The emerging field of lipidomics has been made possible because of advances in mass spectrometry, and in particular tandem mass spectrometry of lipid ions generated by electrospray ionization. The ability to carry out basic biochemical studies of lipids using electrospray ionization is predicated upon understanding the behaviour of lipid derived ions following collision induced decomposition and mechanisms of product ion formation. During the past 20 years, a wealth of information has been generated about lipid molecules that are now analysed by mass spectrometry, however there is no central source where one can obtain basic information about how these very diverse biomolecules behave following collisional activation. This book brings together, in one volume, this information so that investigators considering using tandem mass spectrometry to structurally characterize lipids or to quantitate their occurrence in a biological matrix, will have a convenient source to review mechanism of decomposition reactions related to the diversity of lipid structures.A separate chapter is devoted to each of seven major lipid classes including fatty acids, eicosanoids and bioactive lipid mediators, fatty acyl esters and amides, glycerol esters, glycerophospholipids, sphingolipids, and steroids. Mechanistic details are provided for understanding the pathways of formation of major product ions and ions used for structural characterization. In most cases specific ancillary information has been critical to understand the pathways, including isotope labeling and high resolution analysis of precursor and product ions. For a few specific examples such data is missing and pathways are proposed as a means to initiate further mass spectral experiments to prove or disprove pathway hypotheses. While this work largely centres on the lipid biochemistry of animal (mammalian) systems, general principles can be taken from the specific examples and applied to lipid biochemistry found in plants, fungi, prokaryotes and archeal organisms.