Chromatographic Methods in Metabolomics
[Book Description]
The concept of a metabolic profile was introduced in 1971, when gas chromatography demonstrated a range of compounds present in human samples. Now termed metabolomics, the field is still emerging, and chromatography remains an essential tool for determining metabolites in a living system. This is the first book to present the chromatographic techniques used in metabolomics in a fundamental way. Sample preparation and quality control are described in detail, and all forms of chromatography applied to metabolomics are included. The editors present guidelines on selecting the most appropriate methodology, making the book an accessible guide to anyone entering the field. Handling data and applications are also described. This is an essential handbook for any laboratory looking to embark on a metabolomics research programme and includes the fundamentals of chromatography alongside the latest developments in the field.
[Table of Contents]
Chapter 1 Selection of Analytical 1 (10)
Methodology for Metabolomics
Susanne K. Wiedmer
Tuulia Hyotylainen
1.1 Introduction 1 (5)
1.2 Comparison of Different Methodologies 6 (2)
for Metabolomics
1.3 Conclusion 8 (3)
References 9 (2)
Chapter 2 Sample Collection, Storage and 11 (32)
Preparation
Tuulia Hyotylainen
2.1 Introduction 11 (2)
2.2 Sample Type and Sample Collection 13 (6)
2.2.1 Biofluids 13 (4)
2.2.2 Faecal Samples 17 (1)
2.2.3 Cells 17 (1)
2.2.4 Tissues 18 (1)
2.2.5 Plant Material 18 (1)
2.2.6 Storage and Stability 18 (1)
2.3 Sample Preparation Techniques 19 (13)
2.3.1 Quenching 19 (1)
2.3.2 Drying 20 (1)
2.3.3 Homogenization 20 (2)
2.3.4 Protein Precipitation and Urea 22 (1)
Removal
2.3.5 Extraction 23 (9)
2.4 Clean-up of Extracts 32 (3)
2.5 Derivatization 35 (2)
2.6 Quality Control 37 (2)
2.6.1 Quality Control Samples 38 (1)
2.6.2 Internal Standards/Surrogates 38 (1)
2.7 Conclusion 39 (4)
References 39 (4)
Chapter 3 Mass Spectrometric Detection for 43 (21)
Chromatography
Paivi Poho
Tuulia Hyotylainen
3.1 Introduction 43 (6)
3.2 Mass Spectrometric Instrumentation 49 (6)
3.2.1 MS Interfaces for GC, LC and CE 49 (3)
3.2.2 Mass Analysers 52 (3)
3.3 Identification 55 (4)
3.3.1 GC-MS 57 (1)
3.3.2 LC-MS and CE-MS 58 (1)
3.4 Fluxomics 59 (2)
3.5 Conclusion 61 (3)
References 61 (3)
Chapter 4 Liquid Chromatographic Techniques 64 (23)
in Metabolomics
Georgios A. Theodoridis
Filippos Michopoulos
Helen G. Gika
Robert S. Plumb
Ian D. Wilson
4.1 Introduction 64 (1)
4.2 Liquid Chromatography for Metabolic 65 (1)
Profiling: General Comments
4.3 Formats for Liquid Chromatography 66 (5)
4.3.1 HPLC 66 (1)
4.3.2 UHPLC (UPLC) 67 (1)
4.3.3 Narrow-bore and Capillary LC 67 (2)
(capLC)
4.3.4 Multidimensional LC 69 (1)
4.3.5 Turbulent Flow Chromatography 70 (1)
4.3.6 Supercritical Fluid Chromatography 71 (1)
4.4 Modes of Chromatography 71 (9)
4.4.1 Reversed-Phase Liquid 71 (2)
Chromatography (RPLC)
4.4.2 Hydrophilic Interaction Liquid 73 (3)
Chromatography (HILIC)
4.4.3 Ion-Exchange Liquid 76 (1)
Chromatography (IELC)
4.4.4 Ion-Pair Liquid Chromatography 76 (2)
(IPLC)
4.4.5 Aqueous Normal-phase 78 (1)
Chromatography
4.4.6 Supercritical Fluid Chromatography 78 (2)
4.5 Mass Spectrometry 80 (1)
4.6 Quality Control and Data Analysis 81 (1)
4.7 Biomarker Identification and 82 (1)
Validation
4.8 Conclusion 83 (4)
References 83 (4)
Chapter 5 Gas Chromatographic Techniques in 87 (27)
Metabolomics
Christian J. Wachsmuth
Franziska C. Vogl
Peter J. Oefner
Katja Dettmer
5.1 Introduction 87 (1)
5.2 Sample Preparation 88 (5)
5.2.1 Analysis of Volatile Metabolites 88 (2)
5.2.2 Derivatization of Semi- and 90 (3)
Non-volatile Metabolites
5.3 Principles of GC and MS 93 (4)
5.4 GCxGC-MS 97 (3)
5.5 Identification of Metabolites 100(14)
5.5.1 Gas Chromatography 101(1)
5.5.2 Mass Spectrometry 102(5)
5.5.3 Perspectives 107(1)
Acknowledgement 107(1)
Authorship 107(1)
References 107(7)
Chapter 6 Capillary Electromigration 114(24)
Techniques in Metabolomics
Akiyoshi Hirayama
Tomoyoshi Soga
6.1 Introduction 114(2)
6.2 Technical Considerations 116(9)
6.2.1 CE 116(3)
6.2.2 MS Instrument 119(1)
6.2.3 Interface 119(5)
6.2.4 Chip CE 124(1)
6.3 Data Treatment 125(3)
6.3.1 Data Processing 125(1)
6.3.2 Metabolite Identification 126(2)
6.4 Analytical Strategies 128(5)
6.4.1 Targeted Approach 128(3)
6.4.2 Non-targeted Approach 131(2)
6.5 Conclusion 133(5)
References 133(5)
Chapter 7 Microchip Technology in 138(45)
Metabolomics
Tiina M. Sikanen
7.1 Device Miniaturization Through 138(2)
Microfabrication
7.2 Microchip-based Separation Systems 140(21)
7.2.1 The Choice of the 140(5)
Microfabrication Material
7.2.2 Notes on the Detection Sensitivity 145(3)
7.2.3 Microchip Capillary 148(3)
Electrophoresis
7.2.4 Microchip Liquid Chromatography 151(7)
7.2.5 On-chip Sample Preparation 158(3)
7.3 Microfluidic Enzyme Assays in 161(8)
Metabolomics
7.3.1 Microfluidic Enzyme Reactors 161(3)
7.3.2 Microfluidic Enzyme Assays with 164(3)
MCE Separation
7.3.3 Parallel Microreactors 167(2)
7.3.4 Biomimetic Microreactors 169(1)
7.4 Microfluidic Organomimetic Systems in 169(4)
Metabolomics
7.5 Future Perspectives 173(10)
References 174(9)
Chapter 8 Data Handling 183(12)
Tuulia Hyotylainen
Matej Oresic
8.1 Introduction 183(1)
8.2 Data Acquisition and Handling 184(5)
8.2.1 Peak Detection and Deconvolution 186(2)
8.2.2 Peak Alignment 188(1)
8.2.3 Normalization and Quantification 188(1)
8.3 Quality Control 189(1)
8.4 Processing of Large-scale 190(1)
Metabolomics Data -- Handling of Batch
Effects
8.5 Data Visualization and Analysis 191(1)
8.6 Conclusion 192(3)
References 193(2)
Chapter 9 Applications 195(38)
Paivi Poho
Maarit Kivilompolo
Monica Calderon-Santiago
Sirkku Jantti
Susanne K. Wiedmer
Tuulia Hyotylainen
9.1 Introduction 195(1)
9.2 Lipids 196(12)
9.2.1 Global Profiling of Lipids 197(4)
9.2.2 Targeted Lipid Analyses 201(7)
9.3 Polar Metabolites 208(19)
9.3.1 Global Profiling of Polar 210(4)
Metabolites
9.3.2 Targeted Analysis of Polar 214(13)
Metabolites
9.4 Conclusion 227(6)
References 227(6)
Subject Index 233
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