Plant metabolomics: methods and protocols / edited by Nigel W. Hardy, Robert D. Hall

Incluye bibliografía e índice: páginas 335-340

Practical applications of metabolomics in plant biology.. Part I Material preparation.. Aspects of experimental design for plant metabolomics experiments and guidelines for growth of plant material.. Separating the inseparable: the metabolomic analysis of plant-pathogen interactions.. Precautions for harvest, sampling, storage, and transport of crop plant metabolomics samples.. Tissue preparation using arabidopsis.. Part II Chemical analysis approaches.. Solid phase micro-extraction GC-MS analysis of natural volatile components in melon and rice.. Profiling primary metabolites of tomato fruit with gas chromatography/mass spectrometry.. High-performance liquid chromatography-mass spectrometry analysis of plant metabolites in brassicaceae.. UPLC-MS-based metabolite analysis in tomato.. High precision measurement and fragmentation analysis for metabolite identification.. Fourier transform ion cyclotron resonance mass-spectrometry for plant metabolite profiling and metabolite identification.. Combined NMR and flow injection ESI-MS for brassicaceae metabolomics.. ICP-MS and LC-ICP-MS for analysis of trace elements content and speciation in cereal grains.. The use of genomics and metabolomics methods to quantify fungal endosymbionts and alkaloids in grasses.. Part III Data analysis.. Data (pre- processing of nominal and accurate mass LC-MS or GC-MS data using MetAlign.. TagFinder: preprocessing software for the fingerprinting and the profiling of gas chromatography-mass spectrometry based metabolome analyses.. Chemical identification strategies using liquid chromatography-photodiode array-solid phase extraction-nuclear magnetic resonance/mass spectrometry.. A strategy for selecting data mining techniques in metabolomics.. Index

This book is part of the 'Methods in Molecular Biology' series (no. 860), which is popular for including chapters with introductory notes on the topic, lists of necessary materials and reagents, step-by-step detailed protocols, and key notes on troubleshooting and avoiding common errors. This volume describes several techniques, methods and experimental considerations that are commonly used in the field of plant metabolomics. The field of metabolomics and plant metabolomics has developed significantly during the last 15 years and this book includes contributions by leading authors in the area who played key roles in the development of this field. An introductory chapter describes the field of metabolomics and its growth in the past few years, defines some common terms, and presents the workflow commonly used in metabolomics experiments, from the experimental design to data analysis.The book is divided into three parts that target important topics in any given metabolomics experiment: material preparation, chemical analysis approaches and data analysis. The first chapter of the first section of the book (Chapter 2) includes guidelines on designing metabolomics experiments, not only with regard to the statistical design but also including considerations regarding environmental control, sampling strategy and size of experiment, and potential pitfalls associated with each of these. Chapter 3 presents an interesting protocol not only for the extraction of the metabolome of a plant but also microbial material, which could be applied in the field of plant-microbe interactions. The following chapter expands further on precautions necessary when sampling, transporting and storing biological material, which particularly apply in the field of plant metabolomics where it is common to sample material away from the laboratory. The first part of the book concludes with a chapter dedicated to a protocol for growing arabidopsis plants for metabolomics experiments, highlighting potential issues related to sample storage, sampling time-point strategies and considerations regarding the pooling of biological samples. The second part of the book is dedicated to chemical analysis approaches and contains a series of chapters that describe commonly used methods for the major analytical techniques in plant metabolomics, such as LC-MS and GC-MS. Protocols for GC-MS are presented in Chapters 6 and 7, which describe methods for analysing headspace volatiles and primary metabolites, respectively. This is followed by two chapters with protocols for liquid-chromatography-based mass-spectrometry, the first based on a HPLC system and the second describing a method based on UPLC. Chapters 10 and 11 describe the use of mass spectrometers (Orbitrap, FT-ICR-MS) able to generate an accurate mass fingerprint that can subsequently be used to identify plant metabolites. The following chapter describes a protocol for the extraction of Brassica green tissue and subsequent analysis using a combination of NMR and FI-ESI-MS. eng

Chapter 13 then describes a method for determining the concentrations of trace elements by using LC-ICP-MS in several components of cereal grains. This second part of the volume is concluded with a chapter that integrates the use of genomic and metabolomics approaches to quantify the presence of endophytes and alkaloids in perennial ryegrass. The third part of the book, dedicated to data analysis methods, consists of four chapters. Two of these deal with commonly used pre-processing software, such as MetAlign and TagFinder, and provide detailed instructions regarding their use. Chapter 17 addresses the subject of chemical identification, which is often one of the greatest bottlenecks of any metabolomics study. This particular chapter focuses on strategies used for chemical identification while using LC-MS and LC-SPE-NMR, and showcases how these can be used in combination to provide all the necessary information for structural identification of compounds. This part of the book concludes with a chapter dedicated to data mining techniques that can be used for the analysis of metabolomics datasets. This covers a wide range of data-mining tasks, such as regression, correlation analysis and hypothesis testing, while also providing useful information about matching these data-mining techniques to the goal of the experiment. The chapters presented in this volume stay true to the Methods and Protocols series, with a short piece of background information, a highly detailed step-by-step protocol, and additional practical information that will allow beginners in the field to set up repeatable, high-quality metabolomics experiments. The methods are well illustrated with diagrams, where appropriate, and often include summary tables. 2engThis volume describes a wide range of protocols that use complex techniques routinely used in the field and often refers the reader to other publications for more detailed information about the concepts of the technology used (e.g. MS, NMR and even statistical methods). Describing the technological details is not the goal of this series of books; however, a new user would be advised that the correct interpretation of the results will often require some level of expert assistance and/or further reading about the technologies used. Nevertheless, the wide range of techniques covered will ensure that researchers planning to work or already working in the field will find several chapters of interest in this volume. In summary, this is an excellent addition to the series and can provide much-needed support, especially to scientists starting in the growing field of plant metabolomics. eng