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Mass spectrometry-%%breakStart%%%%breakEnd%%based metabolomics: A practical guide
Trends in Analytical Chemistry 68 (2015) 1
Contents lists available at ScienceDirect
Trends in Analytical Chemistry j o u r n a l h o m e p a g e : w w w. e l s e v i e r. c o m / l o c a t e / t r a c
Book Review Mass Spectrometry-Based Metabolomics: A Practical Guide, Sastia Prama Putri and Eiichiro Fukusaki (Editors), CRC Press, Taylor & Francis Group, 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742, USA, 2015, Hardcover, ISBN: 9781482223767, Price £89. Interest in metabolomics is rapidly expanding in various research fields, such as molecular and chemical biology, biotechnology, drug discovery and development, biomedical sciences and systems pharmacology. Metabolomics provides a direct functional readout of the physiological status of an organism and is in principle ideally suited to describe the health status of an individual. The major aim of metabolomics is to obtain an answer to a biological or clinical question. The analytical workflow used to address a biological question using a metabolomics approach encompasses experimental design, sampling, sample preparation, data acquisition and data analysis. Within this analytical workflow, the design of experiments and sample preparation are key steps as they have a major effect on both the overall coverage and the quality of the metabolomics data obtained and the biological interpretation of the results. In this book, expert researchers pay special attention to these important aspects (Chapters 2 and 3). The design of experiments is considered for both targeted and non-targeted metabolomics studies. Chapter 3 contains well-described protocols with high information content for sample preparation of various biological materials, such as plant leaves, body fluids, tissues and food. The detailed stepby-step sample-preparation protocols are very useful for both nonexperienced and experienced users in the field of metabolomics. I would recommend these protocols for training (under)graduate students in the use of sample-pretreatment techniques for metabolomics studies; these protocols may also be of interest to scientists who want to learn more about the practical aspects of metabolomics research. Considering that the metabolome [i.e., the collection of (endogenous) metabolites present in a given biological sample] is composed of thousands of metabolites with different physico-chemical properties and concentrations, it is evident that multiple complementary analytical techniques should be used for global metabolic profiling studies. Over the past few years, significant developments have been made in analytical techniques, such as nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) mostly coupled to gas chromatography (GC), liquid chromatography (LC) or capillary electrophoresis (CE) for metabolomics studies. This book provides a nice
http://dx.doi.org/10.1016/j.trac.2015.03.003
overview of the role of separation techniques in combination with MS for metabolomics studies. In this context, special emphasis is given on the use of GC-MS and LC-MS for non-targeted and targeted quantitative metabolomics studies (Chapters 4 and 5). Procedures on how to use a particular GC-MS and LC-MS methodology for metabolic profiling studies are given in detail next to data processing of GC-MS and LC-MS data. In the latter case, software tools and programs for alignment of retention times and (multivariate) data analysis are described and complemented by examples of how to use them. Various strategies for metabolite identification are also presented. This book especially pays attention to those MS-based separation techniques (i.e., GC-MS and HPLC-MS) that have proved to be quite robust in the field of metabolomics. State-of-the-art sample-preparation and separation techniques in the field of metabolomics (e.g., nanoscale LC, electrophoretic separation techniques and microfluidics in combination with MS) are described only briefly. A nice feature of this book is that ample attention is devoted to statistical analysis of metabolomics data (Chapter 6). Insight into how to use the various biostatistical tools for large complex data sets is of crucial importance in order to extract the relevant information. General aspects of multivariate and univariate data analysis are considered and (statistical) procedures for data treatment and analysis are provided in a step-by-step manner using a few illustrative examples. The final chapter of the book contains a few case studies that clearly demonstrate how the analytical workflow for metabolomics studies is used for various applications from different research domains. The book contains an in-house library and a built-in software tool, allowing potentially new users to the field to analyze real metabolomics data. Overall, this book considers in a very practical manner and with high information content every aspect of the analytical workflow of a metabolomics study using real, instructive examples. In that context, this book perfectly complements other metabolomics (hand)books that have appeared over the past few years. The content of this book would be highly interesting to a broad range of scientists (i.e., from molecular biologists to biomedical researchers), especially to (undergraduate) students who want to know more about the practical aspects of MS-based metabolomics. Rawi Ramautar * Assistant Professor of Analytical Chemistry, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands * Tel.: +31 (0)71 527 1869 E-mail address: [email protected]
Contents lists available at ScienceDirect
Trends in Analytical Chemistry j o u r n a l h o m e p a g e : w w w. e l s e v i e r. c o m / l o c a t e / t r a c
Book Review Mass Spectrometry-Based Metabolomics: A Practical Guide, Sastia Prama Putri and Eiichiro Fukusaki (Editors), CRC Press, Taylor & Francis Group, 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742, USA, 2015, Hardcover, ISBN: 9781482223767, Price £89. Interest in metabolomics is rapidly expanding in various research fields, such as molecular and chemical biology, biotechnology, drug discovery and development, biomedical sciences and systems pharmacology. Metabolomics provides a direct functional readout of the physiological status of an organism and is in principle ideally suited to describe the health status of an individual. The major aim of metabolomics is to obtain an answer to a biological or clinical question. The analytical workflow used to address a biological question using a metabolomics approach encompasses experimental design, sampling, sample preparation, data acquisition and data analysis. Within this analytical workflow, the design of experiments and sample preparation are key steps as they have a major effect on both the overall coverage and the quality of the metabolomics data obtained and the biological interpretation of the results. In this book, expert researchers pay special attention to these important aspects (Chapters 2 and 3). The design of experiments is considered for both targeted and non-targeted metabolomics studies. Chapter 3 contains well-described protocols with high information content for sample preparation of various biological materials, such as plant leaves, body fluids, tissues and food. The detailed stepby-step sample-preparation protocols are very useful for both nonexperienced and experienced users in the field of metabolomics. I would recommend these protocols for training (under)graduate students in the use of sample-pretreatment techniques for metabolomics studies; these protocols may also be of interest to scientists who want to learn more about the practical aspects of metabolomics research. Considering that the metabolome [i.e., the collection of (endogenous) metabolites present in a given biological sample] is composed of thousands of metabolites with different physico-chemical properties and concentrations, it is evident that multiple complementary analytical techniques should be used for global metabolic profiling studies. Over the past few years, significant developments have been made in analytical techniques, such as nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) mostly coupled to gas chromatography (GC), liquid chromatography (LC) or capillary electrophoresis (CE) for metabolomics studies. This book provides a nice
http://dx.doi.org/10.1016/j.trac.2015.03.003
overview of the role of separation techniques in combination with MS for metabolomics studies. In this context, special emphasis is given on the use of GC-MS and LC-MS for non-targeted and targeted quantitative metabolomics studies (Chapters 4 and 5). Procedures on how to use a particular GC-MS and LC-MS methodology for metabolic profiling studies are given in detail next to data processing of GC-MS and LC-MS data. In the latter case, software tools and programs for alignment of retention times and (multivariate) data analysis are described and complemented by examples of how to use them. Various strategies for metabolite identification are also presented. This book especially pays attention to those MS-based separation techniques (i.e., GC-MS and HPLC-MS) that have proved to be quite robust in the field of metabolomics. State-of-the-art sample-preparation and separation techniques in the field of metabolomics (e.g., nanoscale LC, electrophoretic separation techniques and microfluidics in combination with MS) are described only briefly. A nice feature of this book is that ample attention is devoted to statistical analysis of metabolomics data (Chapter 6). Insight into how to use the various biostatistical tools for large complex data sets is of crucial importance in order to extract the relevant information. General aspects of multivariate and univariate data analysis are considered and (statistical) procedures for data treatment and analysis are provided in a step-by-step manner using a few illustrative examples. The final chapter of the book contains a few case studies that clearly demonstrate how the analytical workflow for metabolomics studies is used for various applications from different research domains. The book contains an in-house library and a built-in software tool, allowing potentially new users to the field to analyze real metabolomics data. Overall, this book considers in a very practical manner and with high information content every aspect of the analytical workflow of a metabolomics study using real, instructive examples. In that context, this book perfectly complements other metabolomics (hand)books that have appeared over the past few years. The content of this book would be highly interesting to a broad range of scientists (i.e., from molecular biologists to biomedical researchers), especially to (undergraduate) students who want to know more about the practical aspects of MS-based metabolomics. Rawi Ramautar * Assistant Professor of Analytical Chemistry, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands * Tel.: +31 (0)71 527 1869 E-mail address: [email protected]