Plant Science Bulletin 58(4) 2012 in the book are scientists active in the EU project META-PHOR and the book´s editors are N. W. Hardy and R. D. Hall. The purpose of this volume is to provide information on basic practical questions concerning experimental work with metabolomics. The book is divided into three parts (Material preparation, Chemical analysis approaches, Data analysis) comprising 18 chapters and explains the terms and concepts used in the field. Chapter 1 describes the practical setting up of a metabolomics experiment, with information on data preprocessing, metabolite identification, data analysis and data reporting. Chapter 2 focuses on questions of experimental design in plant metabolomics experiments and gives guidelines on the growth of plant material. This chapter also describes various philosophical and historical aspects of plant empirical experimentation from Ptolemy, trough Copernicus, and Bacon to Fisher. Observations are also made and on omics experiments and provides a detailed checklist of factors on starting a plant metabolomic experiment. Chapter 3 describes an approach to the co-cultivation of Arabidopsis cell cultures and bacterial plant pathogens to assess dual metabolomics. The Arabidopsis cell cultures, bacterial strains, nutrients, chemicals, antibiotics and the equipment needed are presented in detail. The methods appropriate for such an experiment are also described along with practical recommendations touching research of this kind. The dual metabolomic approach could be adapted to investigate fungal-plant interactions. In chapter 4, the authors recommend various precautions in the preparation and handling of samples from crop plants, and in chapter 5 the methods and material for tissue preparation using Arabidopsis are presented. This chapter ends the Part I (chapters 2-5), which mainly focuses on the preparation of material in metabolomics research, mostly with Arabidopsis as a model plant, and on pathogens. Research experience, methodology and the appropriate laboratory routines are presented. However, a critical reader of the book may be surprised at the absence of any consideration of metabolomics in the context of plant-herbivore interactions or of ecological aspects of symbiotic and antagonistic interactions, or plant signaling. Moreover, no empirical indication of the scientific reliability of the methods described in this part of the book is given, while the sources reveal a certain degree of bias. Part II presents chemical analytical approaches used in metabolomic research. Chapter 6 is
illuminating on solid phase micro-extraction in natural volatile components in melon and rice using gas chromatography-mass spectrometry (GC-MS), and chapter 7 on GC-MS materials and methods for profiling primary metabolites of tomato fruit. Materials and methods for the use of high-perfomance liquid chromatography coupled to mass spectrometry (HPLC-MS) in metabolomics of the plant family Brassicaceae are described in detail in the following chapter. This description is followed by typical chromatographs and their interpretation, and by the practical recommendations for conducting research of this kind. Chapter 9 contains a detailed presentation of tomato metabolite analysis by ultraperfomance liquid chromatography (UPLC), and chapter 10 describes high precision measurement and fragmentation analysis for metabolite identification. All the materials, methods, equipment and standards used in such investigations are presented in depth. Similarly, the succeeding chapters describe Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) for plant metabolite profiling and identification (chapter 11), the use of nuclear magnetic resonance (NMR) and flow injection electrospray mass spectrometry (FI-ESIMS) for metabolomics research in Brassicaceae (chapter 12), and the spectroscopy research protocols of trace element content and speciation in cereal grains (chapter 14). The Part II ends with chapter 14, describing the use of genomics and metabolomics methods to quantify fungal endosymbiots and alkaloids in grasses. A very detailed presentation of the methods and the interpretations of chromatograms greatly help the reader to understand the procedures. Part II (chapters 6-14) of the book is chemical in character and shows the practices and challenges of research in metabolomes. As metabolomes constitute an extremely large field with very diverse groups of molecules, the chemical methods used must be considered case by case. The examples presented in part II are very useful for this purpose. Moreover, readers of the book will benefit from the fact that the methods with many physical and technical parameters and terms of high technology are presented simply and intelligibly. Part III of the book (chapters 15-18) describes data analysis, data interpretation and accuracy estimation. Chapter 15 describes the processing of nominal and accurate mass LC-MS or GC-MS data using the MetAlign software package, and chapter 16 focuses on the methods for the fingerprinting
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