The handbook of plant metabolomics

Tai Lieu Chat Luong

Edited by
Wolfram Weckwerth
and Günter Kahl
The Handbook of Plant
Metabolomics


Titles of the Series “Molecular Plant Biology Handbook Series”
Kahl, G., Meksem, K. (eds.)

The Handbook of Plant Functional Genomics
Concepts and Protocols
2008
ISBN: 978-3-527-31885-8

Meksem, K., Kahl, G. (eds.)

The Handbook of Plant Mutation Screening
Mining of Natural and Induced Alleles
2010
ISBN: 978-3-527-32604-4

Meksem, K., Kahl, G. (eds.)

The Handbook of Plant Genome Mapping
Genetic and Physical Mapping
2005
ISBN: 978-3-527-31116-3

Related Titles
Harbers, M., Kahl, G. (eds.)

Tag-based Next Generation Sequencing
2012
ISBN: 978-3-527-32819-2

Hirt, H. (ed.)

Plant Stress Biology
From Genomics to Systems Biology
2010
ISBN: 978-3-527-32290-9

Hayat, S., Mori, M., Pichtel, J., Ahmad, A. (eds.)

Nitric Oxide in Plant Physiology
2010
ISBN: 978-3-527-32519-1

Kahl, G.

The Dictionary of Genomics, Transcriptomics and Proteomics
2009
ISBN: 978-3-527-32073-8


Edited by Wolfram Weckwerth and Günter Kahl

The Handbook of Plant Metabolomics

The Editors

Prof. Dr. Wolfram Weckwerth
Universität Wien
Molekulare Systembiologie
Althanstr. 14
1090 Wien
Austria
Prof. Dr. Günter Kahl
Mohrmühlgasse 3
63500 Seligenstadt
Germany

Cover Legend
The cover picture presents some structures of
representative phytochemicals and
biosynthetic pathways and enzymes of
Arabidopsis thaliana, referred to in the chapter
“Integrative analysis of secondary metabolism
and transcript regulation in Arabidopsis
thaliana” by Fumio Matsuda and Kazuki Saito
(for further details see Chapter 9, Fig. 4). The
figure was originally published in “Matsuda,
F., et al. (2010) AtMeteEpress development: A
phytochemical atlas of Arabidopsis
development. Plant Physiol, 152, 566–578),
www.plantphysiol.org, # American Society of
Plant Biologists. The permission of the authors

to partly use their figure in a changed format
is greatly appreciated. Foto of Arabidopsis:
# Vasiliy Koval, Fotolia.com

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and author have used their best efforts in preparing this
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limited to special, incidental, consequential, or other
damages.
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Library.
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Nationalbibliothek
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#2013 Wiley-VCH Verlag GmbH & Co. KGaA, Boschstr. 12,
69469 Weinheim, Germany
Wiley-Blackwell is an imprint of John Wiley & Sons, formed

by the merger of Wiley’s global Scientific, Technical, and
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Print ISBN:
ePDF ISBN:
ePub ISBN:
mobi ISBN:
oBook ISBN:

978-3-527-32777-5
978-3-527-66989-9
978-3-527-66990-5
978-3-527-66991-2
978-3-527-66988-2

Cover Design Adam-Design, Weinheim
Typesetting Thomson Digital, Noida, India
Printing and Binding Markono Print Media Pte Ltd,
Singapore
Printed in Singapore
Printed on acid-free paper

Dedicated to
Ulrich and Hannelore Weckwerth
for their endless sympathy, patience and guidance


jVII

Contents
Preface XVII
List of Contributors XIX
Part I

Central Metabolism 1

1

Metabolic Profiling of Plants by GC–MS 3
Camilla B. Hill and Ute Roessner
Introduction 3
Methods and Protocols 7
Sample Preparation 7
Sampling 7
Homogenization and Extraction 7
Procedure for Polar Extraction of Metabolites 8
Chemical Derivatization: Methoxymation and Silylation 9
Procedure for the Chemical Derivatization of Plant Extracts 9
GC–MS Analysis 10
Procedure to Acquire GC–MS Data 11
Data Preprocessing and Export 12
Procedure for Postacquisition Data Preprocessing 12

Data Analysis and Statistics 14
Procedure for Postacquisition Data Analysis 15
Applications of the Technology 15
Perspectives 17
References 18

1.1
1.2
1.2.1
1.2.1.1
1.2.1.2
1.2.1.3
1.2.2
1.2.2.1
1.2.3
1.2.3.1
1.2.4
1.2.4.1
1.2.4.2
1.2.4.3
1.3
1.4
2

2.1
2.2
2.2.1
2.2.2

Isotopologue Profiling – Toward a Better Understanding

of Metabolic Pathways 25
Wolfgang Eisenreich, Claudia Huber, Erika Kutzner, Nihat Knispel,
and Nicholas Schramek
Introduction 25
Methods and Protocols to Determine Isotopologues 31
Mass Spectrometry 31
Protocols for Isotopologue Profiling by GC–MS 36


VIII

j Contents
2.2.2.1
2.2.2.2
2.2.2.3
2.2.3
2.2.4
2.2.5
2.2.6
2.3
2.3.1
2.3.2
2.4

Protein-Bound Amino Acids 36
Metabolic Intermediates and Polar Products 37
Carbohydrates 37
NMR Spectroscopy 38
Protocols for Isotopologue Profiling by NMR 41
Deconvolution of Isotopologue Data 43

Expanding the Metabolic Space by Retrobiosynthetic Analysis 45
Applications 46
Experiments Using ½U-13 C6 Glucose 46
Experiments Using 13 CO2 47
Perspectives 53
References 54

3

Nuclear Magnetic Resonance Spectroscopy for Plant
Metabolite Profiling 57
Sonia van der Sar, Hye Kyong Kim, Axel Meissner, Robert Verpoorte,
and Young Hae Choi
Introduction 57
Methods and Protocols 59
Sample Preparation 59
Harvesting Plant Material 60
Drying 60
Extraction 60
Data Acquisition 60
Standard 1H-NMR Spectroscopy 61
J-Resolved Spectroscopy 61
Data Analysis 61
Applications 62
1D 1H-NMR Spectroscopy 62
2D NMR Spectroscopy 63
J-Resolved Spectroscopy 65
COSY and TOCSY 67
HMBC and HMQC/HSQC 68
NOESY or ROESY (CAMELSPIN) 69

DOSY 69
Magic Angle Spinning 70
Perspectives 71
References 72

3.1
3.2
3.2.1
3.2.1.1
3.2.1.2
3.2.1.3
3.2.2
3.2.3
3.2.4
3.2.5
3.3
3.3.1
3.3.2
3.3.2.1
3.3.2.2
3.3.2.3
3.3.2.4
3.3.2.5
3.3.3
3.4

4

4.1
4.2

Comprehensive Two-Dimensional Gas Chromatography
for Metabolomics 77
Katja Dettmer, Martin F. Almstetter, Christian J. Wachsmuth,
and Peter J. Oefner
Introduction 77
Methods and Protocols 81


Contents

4.2.1
4.2.2
4.2.3
4.2.4
4.2.5
4.3
4.3.1
4.3.2
4.4

Instrumentation 81
Sample Preparation and Analysis 82
Data Processing 83
Metabolic Fingerprinting 83
Quantitative Analysis of Selected Metabolites 84
Applications of the Technology 85
Data Analysis 85
Literature 88
Perspectives 89

References 90

5

MALDI Mass Spectrometric Imaging of Plants 93
Ale9s Svato9s and Hans-Peter Mock
Introduction 93
Sample Preparation 96
Data Acquisition 98
Data Processing 98
Methods and Protocols 99
Sample Preparation and Handling 99
Intact Tissues 99
Cryosectioning 99
Matrix Deposition 100
Paintbrush (Figure 5.2) 100
Sublimation (Figure 5.3) 102
MALDI-MS Imaging Measurement 103
Bruker Ultraflex Instruments 103
Waters MALDI Micro MX 104
Imaging Intact Tissues and Objects 105
Future Perspectives 109
References 109

5.1
5.1.1
5.1.2
5.1.3
5.2
5.2.1

5.2.1.1
5.2.1.2
5.2.2
5.2.2.1
5.2.2.2
5.2.3
5.2.3.1
5.2.3.2
5.3
5.4

6

6.1
6.2
6.2.1
6.2.2
6.2.3
6.2.4
6.2.5
6.2.6
6.2.7

Medicago truncatula Root and Shoot Metabolomics: Protocol
for the Investigation of the Primary Carbon and Nitrogen Metabolism
Based on GC–MS 111
Vlora Mehmeti, Lena Fragner, and Stefanie Wienkoop
Introduction 111
Methods and Protocols 112
Equipment and Software 112

Buffers and Chemicals 112
Plant Material and Harvest 113
Extraction 114
Derivatization 115
GC–MS Setup for the Analysis 115
Metabolite Identification and Quantification: Data Matrix
Processing 116

jIX


j Contents

X

6.2.8
6.3
6.4

Data Mining 119
Applications of the Technology 119
Perspectives 121
References 123

Part II

Secondary and Lipid Metabolism 125

7

Study of the Volatile Metabolome in Plant–Insect Interactions 127
Georg J.F. Weingart, Nora C. Lawo, Astrid Forneck, Rudolf Krska,
and Rainer Schuhmacher
Introduction 127
Plant–Insect Interactions 127
Significance of Volatile Plant Metabolites 128
Study of the Plant Volatile Metabolome in Plant–Insect Interactions 128
Setting Up of Biological Experiments 129
Sampling, Quenching, and Sample Preparation 130
Headspace Extraction and Measurement by GC–MS 131
Data Handling 134
Biological Interpretation 135
Methods and Protocols 135
Permanent Breed of Insects 135
Cultivation of Grapevine Plants and Inoculation with Phylloxera 136
Materials 136
Procedures 136
Sampling and Quenching of Plant Tissue (Roots and Leaves) 138
Sampling and Quenching of Root Tips 138
Sampling and Quenching of Grapevine Leaves 139
Milling and Weighing of Plant Tissue (Roots and Leaves) 140
Milling and Weighing of Root Samples 140
Milling and Weighing of Leaf Samples 141
Measurement – Automated HS-SPME Extraction
and GC–MS Analysis 143
Materials 143
SPME Method 143
GC Method 144
MS Settings 144
Data Processing with AMDIS 145

An In-House Reference Library Has to be Established in Advance 145
Generation of RI Calibration File 146
Batch Job Analysis for the Simultaneous Processing of Multiple
Sample Chromatograms 146
Statistics/Chemometrics 147
Univariate Statistics 147
Multivariate Statistics 148

7.1
7.1.1
7.1.2
7.1.3
7.1.3.1
7.1.3.2
7.1.3.3
7.1.3.4
7.1.3.5
7.2
7.2.1
7.2.2
7.2.2.1
7.2.2.2
7.2.3
7.2.3.1
7.2.3.2
7.2.4
7.2.4.1
7.2.4.2
7.2.5
7.2.5.1

7.2.5.2
7.2.5.3
7.2.5.4
7.2.6
7.2.6.1
7.2.6.2
7.2.6.3
7.2.7
7.2.7.1
7.2.7.2


Contents

7.3
7.4

Applications of the Technology 148
Perspectives 149
References 150

8

Metabolomics in Herbal Medicine Research 155
Lie-Fen Shyur, Chiu-Ping Liu, and Shih-Chang Chien
Introduction 155
Methods and Protocols 158
Materials 158
Reagents 158
Equipment 159

Procedures 160
Sample Handling for Medicinal Plants 160
Sample Preparation for LC–MS Analysis 160
LC–MS Analysis 161
HPLC–Photodiode Array (PDA) MS Setup and Analysis 161
GC–MS Analysis 162
Plant Extract Preparation for GC–MS Analysis 163
GC–MS Parameters and Analysis 164
LC–MS and GC–MS Data Analysis 165
LC–SPE–NMR Analysis 166
Sample Preparation and LC–SPE–NMR Analysis 167
HPLC–SPE–NMR Data Analysis 168
Applications 168
Perspectives 169
References 170

8.1
8.2
8.2.1
8.2.1.1
8.2.1.2
8.2.2
8.2.2.1
8.2.2.2
8.2.2.3
8.2.2.4
8.2.2.5
8.2.2.6
8.2.2.7
8.2.2.8

8.2.2.9
8.2.2.10
8.2.2.11
8.3
8.4

9

9.1
9.2
9.2.1
9.2.1.1
9.2.1.2
9.2.1.3
9.2.2
9.2.2.1
9.2.2.2
9.2.3
9.2.3.1
9.2.3.2
9.2.3.3

Integrative Analysis of Secondary Metabolism and Transcript
Regulation in Arabidopsis thaliana 175
Fumio Matsuda and Kazuki Saito
Introduction 175
Methods and Protocols 177
Metabolome Analysis of Plant Secondary Metabolites 177
Sample Preparation 177
Data Acquisition 178

Preparation of Metabolite Accumulation Data from the Raw
Chromatogram Data 179
Preparation of Combined Data Matrix 180
Preparation of Gene Expression Data 180
Combination of Data Matrices 180
Data Mining 180
BL-SOM Analysis 180
Correlation Analysis 181
Principal Component Analysis and Application of Other
Data Mining Techniques 183

jXI


XII

j Contents
9.3
9.4

Applications of the Technology 183
Perspectives 187
References 190

10

Liquid Chromatographic–Mass Spectrometric Analysis of
Flavonoids 197
Maciej Stobiecki and Piotr Kachlicki
Introduction 197

Role of Flavonoids and Their Derivatives in Biological Systems 197
Preparation of Biological Material for Metabolomic Analysis and/or
Metabolite Profiling 199
Instrumental Considerations 201
Methods and Protocols: Liquid Chromatography–Mass
Spectrometry of Flavonoids 206
General Remarks 206
Plant Cultivation Conditions 208
Preparation of Biological Material with Biotechnological Methods
(Callus, Cell, or Hairy Root Cultures) 208
Extraction of Plant Tissue or Biotechnologically Prepared Material 208
Extraction Procedure 209
Solid-Phase Extraction of Culture Medium or Apoplastic Fluids 209
Preparation of Samples for LC–MS Analyses 210
Chromatographic Protocols for Separation of Flavonoid
Glyconjugates 210
Control of Ionization Parameters During Mass Spectrometric
Analysis and Identification of Compounds During LC–MS
Metabolite Profiling 211
Applications of the Technology 211
Perspectives 211
References 212

10.1
10.1.1
10.1.2
10.1.3
10.2
10.2.1
10.2.2

10.2.3
10.2.4
10.2.4.1
10.2.5
10.2.6
10.2.7
10.2.8

10.3
10.4

11

11.1
11.2
11.2.1
11.2.2
11.2.3
11.2.4
11.2.5
11.2.6
11.2.7
11.2.8
11.2.8.1

Introduction to Lipid (FAME) Analysis in Algae Using Gas
Chromatography–Mass Spectrometry 215
Takeshi Furuhashi and Wolfram Weckwerth
Introduction 215
Methods and Experimental Protocol 216

Extraction 216
Bound and Free Fatty Acids 217
Pigments 217
Contaminants 219
Derivatization 219
GC–MS System 220
Identification 220
Protocols 221
Protocol I 221


Contents

11.2.8.2
11.2.9
11.3

Protocol II 221
GC–MS Instrument and Conditions 223
Application and Perspective 223
References 224

12

Multi-Gene Transformation for Pathway Engineering of Secondary
Metabolites 227
Hideyuki Suzuki, Eiji Takita, Kiyoshi Ohyama, Satoru Sawai, Hikaru Seki,
Nozomu Sakurai, Toshiya Muranaka, Masao Ishimoto, Hiroshi Sudo,
Kazuki Saito, and Daisuke Shibata
12.1

Introduction 227
12.2
Methods and Protocols 233
12.2.1
Chemicals 233
12.2.2
Plasmid Construction of Multi-Gene Transformation 233
12.2.3
Preparation of Dual Terminator (DT) Fragment by PCR-Based
Overlap Extension Method 233
12.2.4
Plasmid Construction of pUHR KS CSPS Thsp 236
12.2.5
Construction of pHSG299 CSPS 35S-CYP88-DT (Figure 12.2a) 236
12.2.6
Construction of pHSG299 CSPS 35S-CYP72-DT2 (Figure 12.2a) 237
12.2.7
Construction of pHSG299-CYP93(RNAi)-DT (Figure 12.2a) 238
12.2.8
Construction of pUHR KS CSPS Thsp-CYP88-CYP72-CYP93
(RNAi) 239
12.2.9
Transformation of Soybean by Particle Bombardment 239
12.2.9.1 Preparation of Embryogenic Suspension Tissue Culture 239
12.2.9.2 Preparation of Plasmid DNA for Particle Bombardment 240
12.2.9.3 Conditions of Particle Bombardment 240
12.2.9.4 Selection and Generation of Transgenic Soybean Plants 240
12.2.10
GC-MS Analysis for Triterpene Glycone 241
12.2.10.1 Extraction of Metabolite 241

12.2.10.2 Acid Treatment of Extracted Metabolites 241
12.2.10.3 Derivatization of Metabolites 242
12.2.11
GC-MS Conditions 242
12.3
Application of Technology 242
12.4
Perspectives 243
References 243
Part III

Metabolomics and Genomics 245

13

Metabolomics-Assisted Plant Breeding 247
Alexander Herrmann and Nicolas Schauer
Introduction 247
Method 249
Applications of the Technology 251
Perspective 253
References 254

13.1
13.2
13.3
13.4

jXIII

XIV

j Contents
14
14.1
14.2
14.2.1
14.2.2
14.2.2.1
14.2.2.2
14.2.3
14.2.3.1
14.2.3.2
14.2.3.3
14.2.3.4
14.2.4
14.2.5
14.2.6
14.2.6.1
14.2.6.2
14.2.6.3
14.2.6.4
14.2.6.5
14.2.7
14.2.8
14.2.8.1
14.2.8.2
14.3
14.4

Conducting Genome-Wide Association Mapping of Metabolites 255
Susanna Atwell and Daniel J. Kliebenstein
Introduction 255
Methods and Protocols 256
Biological Question to Be Addressed 256
Chemistry to Study 256
Chemical Class 256
Extraction and Detection Platform 257
Species Choice 258
Genotypic Choices 258
GWA Populations Available 259
Domestication Status 260
Ability to Conduct Appropriate Follow-Up Experiments 260
Should I Utilize an Additional Perturbation? 260
Conducting the Phenotype Measurements 261
Computational Platform to Use for Analysis 261
Single Marker Analysis 262
Population Structure Modification 262
Resulting GWA Plots 262
Gene-Based Approaches 263
What Should I Use and How Do I Use It? 263
Candidate Gene Selection 265
Candidate Gene Validation 266
Validate That the Gene Influences the Phenotype? 267
Validate That Natural Variation in the Gene Influences the
Phenotype 267
Applications 267
Perspectives 268
References 268

Part IV

Metabolomics and Bioinformatics 273

15

Metabolite Clustering and Visualization of Mass Spectrometry Data
Using One-Dimensional Self-Organizing Maps 275
Alexander Kaever, Manuel Landesfeind, Kirstin Feussner, Ivo Feussner,
and Peter Meinicke
Introduction 275
Methods and Protocols 276
Data Import 277
Clustering 277
Cluster Analysis 280
Applications of the Technology 281
Perspectives 286
References 286

15.1
15.2
15.2.1
15.2.2
15.2.3
15.3
15.4


Contents

16
16.1
16.2
16.2.1
16.2.2
16.2.3
16.2.4
16.2.5
16.3

17
17.1
17.2
17.2.1
17.2.1.1
17.2.1.2
17.2.1.3
17.2.1.4
17.2.1.5
17.2.2
17.2.2.1
17.2.2.2
17.2.2.3
17.2.3
17.2.3.1
17.2.3.2
17.2.3.3
17.2.4
17.2.4.1

17.2.4.2
17.2.5
17.2.5.1
17.2.5.2
17.3
17.4

Metabolite Identification and Computational Mass Spectrometry 289
Steffen Neumann, Florian Rasche, Sebastian Wolf, and Sebastian B€ocker
Introduction 289
Annotation and Identification of Metabolites 290
Exact Mass Search in Compound Libraries 291
Deriving the Elemental Composition from MS1 292
Elemental Composition from MS2 and MSn 293
In Silico Library Search with MetFrag 294
Reference Spectral Library Lookup 299
Perspectives 302
References 303
Using COVAIN to Analyze Metabolomics Data 305
Xiaoliang Sun and Wolfram Weckwerth
Introduction 305
Methods 308
Data Preprocessing 308
Imputation of Missing Values 308
Transformations to Satisfy Prerequisites of Statistical Methods 310
Adjusting Outliers 310
Scaling 310
Filtering by Statistical Features 310
Uni- and Bivariate Statistical Methods for Individual
Metabolite-Level Analysis 311

ANOVA Compares Single Metabolite Levels 311
Correlation Coefficients Interpret the Relationships Between
Pairwise Two Metabolites 311
Granger Causality Analysis Identifies the Causation Between
Pairwise Two Metabolites in Time-Series Data 311
Multivariate Statistical Methods for Group-Level Analysis 312
PCA Distinguishes Phenotypes and Finds Most Influencing
Metabolites 312
Independent Component Analysis Distinguishes Phenotypes
and Finds the Latent Sources of Metabolites in Time-Series Data 312
Clustering Classifies Data Into Groups 312
Network-Level Analysis 313
Network Mapping 313
Network Inference 313
Influences of Data Preprocessing on Statistical Analysis Results 313
On the Mean Values: ANOVA, Correlation Coefficient, Granger
Analysis, and Clustering 313
On the Variance and Covariance: ANOVA, PCA, and ICA 314
Application 314
Perspective 320
References 320

jXV


XVI

j Contents
18

18.1
18.2
18.2.1
18.2.2
18.2.3
18.2.3.1
18.2.3.2
18.2.4
18.2.4.1
18.2.4.2
18.2.4.3
18.2.5
18.2.5.1
18.2.5.2
18.2.6
18.3

Mass Spectral Search and Analysis Using the Golm Metabolome
Database 321
Jan Hummel, Nadine Strehmel, Christian B€olling, Stefanie Schmidt,
Dirk Walther, and Joachim Kopka
Introduction 321
Methods and Protocols: the GMD and Supported Data Analysis
Workflows 322
The GMD Data Entities 322
The Text Search Queries 325
The Mass Spectrum Query Submission and Analysis Options 325
Mass Spectral Matching 326
Decision Tree (DT)-Supported Substructure Prediction 329
Interpreting the Mass Spectral Analysis Results 329

The Mass Spectral Matching Results 329
The Substructure Prediction Results 332
Interpreting Decision Trees 333
The Web Services at GMD 336
General Considerations 336
The GMD Web Service Modules 337
The GMD Download Options 338
Applications and Perspectives 341
References 342
Glossary 345
Index 415


jXVII

Preface
Whereas the most modern topics of plant research, grouped into the term “omics,”
such as genomics, transcriptomics, and proteomics, are comparatively new, the
strategies to isolate, purify, identify, and quantify a multitude of low molecular
weight cellular compounds (called metabolites) look back onto a long history. While
initially only metabolites present in comparatively high concentrations could be
isolated and quantified (sometimes only semiquantified), the advent of enzymatic
detection techniques in the 1970s brought a breakthrough in precise metabolite
analysis. Unfortunately, these techniques required the coupling of a metabolites
detection to the reduction/oxidation of NADỵ or NADPỵ, and therefore excluded
the majority of metabolites, especially secondary metabolites. More recent developments in mass spectrometry (MS), matrix-assisted laser desorption/ionization
(MALDI)–MS for metabolite imaging, gas chromatography coupled to mass spectrometry (GC–MS), liquid chromatography coupled to mass spectrometry (LC–MS),
and NMR technology for medium- to high-throughput identification and quantification of low molecular weight compounds pushed metabolite analysis to today’s
advanced level, where various physico-chemical separation techniques are combined to analyze metabolite profiles in considerable detail and accuracy. The present
state of technology for metabolite analysis has been denoted “metabolomics.”

Metabolomics reflects the physiological state of an organism or its organs, tissues,
or cells, and therefore allows a hitherto not possible comprehensive understanding
of the biology of an organism and its response to intrinsic or environmental changes
or influences. The various techniques of metabolomics allow the comprehensive
profiling of cellular metabolites at the systems level, thereby providing a direct
readout of biochemical activity that can be correlated with phenotype and used to
identify therapeutic targets. This omics discipline then bridges the gap between
genotype and phenotype. The present Handbook of Plant Metabolomics not only
witnesses the present state-of-the-art metabolomics and its widespread applications,
but also portrays up-to-date technical advances in metabolic fingerprinting and the
in silico analysis of the resulting, mostly very complex, metabolite patterns.
The Handbook of Plant Metabolomics (Metabolite Profiling and Networking) is the
fourth volume in the successful Wiley-VCH series of Handbooks of Plant Genome
Analysis, and follows the warmly welcomed The Handbook of Plant Genome Mapping
(Genetic and Physical Mapping), The Handbook of Plant Functional Genomics


XVIII

j Preface
(Concepts and Protocols), and The Handbook of Plant Mutation Screening (Mining of
Natural and Induced Alleles). It provides informative introductions to each chapter,
detailed descriptions of techniques for metabolite profiling, and robust and ready-togo laboratory protocols, in addition to some applications, all written by internationally renowned experts in their research fields. Although this volume focuses on plant
metabolomics, the techniques presented are broadly applicable to other biological
systems exemplifying the pioneering and original character of metabolomics in
plant biology. This rapid development of metabolomics to a mature technology is
catalyzing the application of metabolomics in other fields of research also, such as
biomedicine.
The Editors very much appreciate the excellent chapters contributed by all the
authors, and expect that The Handbook of Plant Metabolomics will reproduce the

worldwide success of its three progenitors.
Vienna (Austria)
Frankfurt am Main (Germany)
August 2012

Wolfram Weckwerth
G€
unter Kahl


jXIX

List of Contributors
Martin F. Almstetter
University of Regensburg
Institute of Functional Genomics
Josef-Engert-Strasse 9
93053 Regensburg
Germany
Susanna Atwell
University of California, Davis
Department of Plant Sciences
One Shields Avenue
Davis, CA 95616
USA
Sebastian B€ocker
Friedrich-Schiller-University Jena
Institute for Informatics
Ernst-Abbe-Platz 2
07743 Jena

Germany
Christian B€olling
Charite Universit€atsmedizin Berlin
Computational Systems
Biochemistry Group
Seestrasse 73
13347 Berlin
Germany

Shih-Chang Chien
National Chung Hsing University
Experimental Forest Management
Office
No. 250, Kuo Kuang Road
Taichung 402
Taiwan
Young Hae Choi
Leiden University
Institute of Biology
Natural Products Laboratory
Sylviusweg 72, 2333 BE
Leiden
The Netherlands
Katja Dettmer
University of Regensburg
Institute of Functional Genomics
Josef-Engert-Strasse 9
93053 Regensburg
Germany
Wolfgang Eisenreich

Technische Universit€at M€
unchen
Lehrstuhl f€
ur Biochemie
Lichtenbergstrasse 4
85435 Garching
Germany


j List of Contributors

XX

Ivo Feussner
Georg-August-Universität Göttingen
Albrecht-von-Haller-Institute for
Plant Sciences
Department of Plant Biochemistry
Justus-von-Liebig-Weg 11
37077 Göttingen
Germany
Kirstin Feussner
Georg-August-Universität Göttingen
Institute of Microbiology and
Genetics
Department of Molecular
Microbiology and Genetics
Grisebachstrasse 8
37077 Göttingen
Germany

and
Georg-August-Universität Göttingen
Albrecht-von-Haller-Institute for
Plant Sciences
Department of Plant Biochemistry
Justus-von-Liebig-Weg 11
37077 Göttingen
Germany

Takeshi Furuhashi
University of Vienna
Department of Molecular Systems
Biology (MOSYS)
Althanstrasse 14
1090 Vienna
Austria
Alexander Herrmann
Metabolomic Discoveries GmbH
Am M€
uhlenberg 11
14476 Potsdam-Golm
Germany
Camilla B. Hill
The University of Melbourne
School of Botany, Building 122
Australian Centre for Plant
Functional Genomics (ACPFG)
Professors Walk
Parkville, VIC 3052
Australia

Claudia Huber
Technische Universit€at M€
unchen
Lehrstuhl f€
ur Biochemie
Lichtenbergstrasse 4
85435 Garching
Germany

Astrid Forneck
University of Natural Resources and
Life Sciences, Vienna
Department of Crop Sciences
Division of Viticulture and Pomology
Konrad-Lorenz-Strasse 24
3430 Tulln
Austria

Jan Hummel
Max Planck Institute of Molecular
Plant Physiology (MPIMP)
Bioinformatics Group
Am Muehlenberg 1
14476 Potsdam-Golm
Germany

Lena Fragner
University of Vienna
Department of Molecular Systems
Biology

Althanstrasse 14
1090 Vienna
Austria

Masao Ishimoto
National Institute of Agrobiological
Sciences
2-1-2 Kannondai
Tsukuba
Ibaraki 305-8602
Japan


List of Contributors

Piotr Kachlicki
Institute of Plant Genetics PAS
Strzeszy
nska 34
60-479 Pozna
n
Poland
Alexander Kaever
Georg-August-Universität Göttingen
Institute of Microbiology and
Genetics
Department of Bioinformatics
Goldschmidtstrasse 1
37077 Göttingen
Germany

Hye Kyong Kim
Leiden University
Institute of Biology
Natural Products Laboratory
Sylviusweg 72, 2333 BE
Leiden
The Netherlands
Daniel J. Kliebenstein
University of California, Davis
Department of Plant Sciences
One Shields Avenue
Davis, CA 95616
USA
Nihat Knispel
Technische Universit€at M€
unchen
Lehrstuhl f€
ur Biochemie
Lichtenbergstrasse 4
85435 Garching
Germany
Joachim Kopka
Max Planck Institute of Molecular
Plant Physiology
Applied Metabolome Analysis
Department 1
Prof. Lothar Willmitzer
Am Muehlenberg 1
D-14476 Potsdam-Golm
Germany

Rudolf Krska
University of Natural Resources and
Life Sciences, Vienna
Center for Analytical Chemistry
Department IFA-Tulln
Konrad-Lorenz-Strasse 20
3430 Tulln
Austria
Erika Kutzner
Technische Universit€at M€
unchen
Lehrstuhl f€
ur Biochemie
Lichtenbergstrasse 4
85435 Garching
Germany
Manuel Landesfeind
Georg-August-Universität Göttingen
Institute of Microbiology and Genetics
Department of Bioinformatics
Goldschmidtstrasse 1
37077 Göttingen
Germany
Nora C. Lawo
University of Natural Resources and
Life Sciences, Vienna
Division of Viticulture and Pomology
Department of Crop Sciences
Konrad-Lorenz-Strasse 24

3430 Tulln
Austria
and
Syngenta Crop Protection
Research Stein
Schaffhauserstrasse 101
4332 Stein
Switzerland

jXXI


XXII

j List of Contributors
Chiu-Ping Liu
National Taiwan University
Institute of Biotechnology
No. 1, Sec. 4, Roosevelt Road
Taipei 10617
Taiwan
Fumio Matsuda
RIKEN Plant Science Center
Metabolomic Function Research Group
Suehiro-cho 1-7-22
Tsurumi-ku
Yokohama 230-0045
Japan
and
Osaka University

Graduate School of Information
Science and Technology
Department of Bioinformatic
Engineering
1-5, Yamada-oka Suita
Osaka 565-0871
Japan

Axel Meissner
Leiden University Medical Center
Department of Parasitology
P.O. Box 9600
Eindhovenweg 20, 2333 ZC
Leiden
The Netherlands
Hans-Peter Mock
Leibniz Institute of Plant Genetics
and Crop Plant Research (IPK)
Corrensstrasse 3
06466 Gatersleben
Germany
Toshiya Muranaka
Yokohama City University
Kihara Institute for Biological
Research
641-12 Maioka-cho
Totsuka-ku
Yokohama
Kanagawa 244-0813
Japan

and

Vlora Mehmeti
University of Vienna
Department of Molecular Systems
Biology
Althanstrasse 14
1090 Vienna
Austria

Osaka University
Department of Biotechnology
2-1 Yamadaoka
Suita-shi
Osaka 565-0871
Japan

Peter Meinicke
Georg-August-Universität Göttingen
Institute of Microbiology and
Genetics
Department of Bioinformatics
Goldschmidtstrasse 1
37077 Göttingen
Germany

Steffen Neumann
Leibniz Institute of Plant
Biochemistry, IPB Halle
Department of Stress and

Developmental Biology
Weinberg 3
06120 Halle (Saale)
Germany


List of Contributors

Peter J. Oefner
University of Regensburg
Institute of Functional Genomics
Josef-Engert-Strasse 9
93053 Regensburg
Germany
Kiyoshi Ohyama
Tokyo Institute of Technology
Graduate School of Engineering
2-12-1 Ohokayama
Meguro-ku
Tokyo 152-8551
Japan
and
RIKEN Plant Science Center
1-7-22 Suehiro-cho
Tsurumi-ku
Yokohama
Kanagawa 230-0045
Japan
Florian Rasche
Friedrich-Schiller-University Jena

Institute for Informatics
Ernst-Abbe-Platz 2
07743 Jena
Germany
Ute Roessner
The University of Melbourne
School of Botany, Building 122
Australian Centre for Plant
Functional Genomics (ACPFG) and
Metabolomics Australia
Professors Walk
Parkville, VIC 3052
Australia

Kazuki Saito
RIKEN Plant Science Center
Metabolomic Function Research
Group
Suehiro-cho 1-7-22
Tsurumi-ku
Yokohama 230-0045
Japan
and
Graduate School of Pharmaceutical
Sciences
Department of Molecular Biology and
Biotechnology
Chiba University
Inohana 1-8-1
Chuo-ku

Chiba 260-8675
Japan
Nozomu Sakurai
Kazusa DNA Research Institute
2-6-7 Kazusa-Kamatari
Kisarazu
Chiba 292-0818
Japan
Satoru Sawai
Chiba University
Graduate School of Pharmaceutical
Sciences
1-33 Yayoi-cho
Inage-ku
Chiba 263-8522
Japan
and
Tokiwa Phytochemical Co., Ltd.
58 Kinoko
Sakura
Chiba 285-0801
Japan

jXXIII


XXIV

j List of Contributors
and

RIKEN Plant Science Center
1-7-22 Suehiro-cho
Tsurumi-ku
Yokohama
Kanagawa 230-0045
Japan
Nicolas Schauer
Metabolomic Discoveries GmbH
Am M€
uhlenberg 11
14476 Potsdam-Golm
Germany
Stefanie Schmidt
Max Planck Institute of Molecular
Plant Physiology
Applied Metabolome Analysis
Department 1
Prof. Lothar Willmitzer
Am Muehlenberg 1
D-14476
Potsdam-Golm
Germany
Nicholas Schramek
Technische Universit€at M€
unchen
Lehrstuhl f€
ur Biochemie
Lichtenbergstrasse 4
85435 Garching
Germany

and
Bavarian Health and Food Safety
Authority
Veterin€arstrasse 2
85764 Oberschleissheim
Germany

Rainer Schuhmacher
University of Natural Resources and
Life Sciences, Vienna
Center for Analytical Chemistry
Department IFA-Tulln
Konrad-Lorenz-Strasse 20
3430 Tulln
Austria
Hikaru Seki
Yokohama City University
Kihara Institute for Biological
Research
641-12 Maioka-cho
Totsuka-ku
Yokohama
Kanagawa 244-0813
Japan
and
Osaka University
Department of Biotechnology
2-1 Yamadaoka
Suita-shi
Osaka 565-0871

Japan
Daisuke Shibata
Kazusa DNA Research Institute
2-6-7 Kazusa-Kamatari
Kisarazu
Chiba 292-0818
Japan
Lie-Fen Shyur
Agricultural Biotechnology Research
Center
Academia Sinica
No. 128, Sec. 2, Academia Road
Nankang
Taipei 115
Taiwan


List of Contributors

Maciej Stobiecki
Institute of Bioorganic Chemistry
PAS
Noskowskiego 12/14
Laboratory of Natural Products
Biochemistry
61-704 Pozna
n
Poland
Nadine Strehmel
Leibniz Institute of Plant

Biochemistry, IPB Halle
Department of Stress and
Developmental Biology
Weinberg 3
06120 Halle (Saale)
Germany
Hiroshi Sudo
Chiba University
Graduate School of Pharmaceutical
Sciences
1-33 Yayoi-cho
Inage-ku
Chiba 263-8522
Japan
and
Tokiwa Phytochemical Co., Ltd.
58 Kinoko
Sakura
Chiba 285-0801
Japan
and
Hoshi University
School of Pharmacy and
Pharmaceutical Sciences
2-4-41 Ebara
Shinagawa-ku
Tokyo 142-8501
Japan

Xiaoliang Sun

University of Vienna
Department of Molecular Systems
Biology
Althanstrasse 14
1090 Vienna
Austria
Hideyuki Suzuki
Kazusa DNA Research Institute
2-6-7 Kazusa-Kamatari
Kisarazu
Chiba 292-0818
Japan
Ale9s Svato9s
Max Planck Institute for Chemical
Ecology
Mass Spectrometry Research Group
Hans-Knoell-Strasse 8
07745 Jena
Germany
Eiji Takita
Kazusa DNA Research Institute
2-6-7 Kazusa-Kamatari
Kisarazu
Chiba 292-0818
Japan
and
Idemitsu Kosan Co., Ltd.
1280 Kamiizumi
Sodegaura-shi
Chiba 299-0293

Japan
Sonia van der Sar
Leiden University
Institute of Biology
Natural Products Laboratory
Sylviusweg 72, 2333 BE
Leiden
The Netherlands

jXXV


XXVI

j List of Contributors
Robert Verpoorte
Leiden University
Institute of Biology
Natural Products Laboratory
Sylviusweg 72, 2333 BE
Leiden
The Netherlands
Christian J. Wachsmuth
University of Regensburg
Institute of Functional Genomics
Josef-Engert-Strasse 9
93053 Regensburg
Germany
Dirk Walther
Max Planck Institute of Molecular

Plant Physiology (MPIMP)
Bioinformatics Group
Am Muehlenberg 1
14476 Potsdam-Golm
Germany
Wolfram Weckwerth
University of Vienna
Department of Molecular Systems
Biology
Althanstrasse 14
1090 Vienna
Austria

Georg J.F. Weingart
University of Natural Resources and
Life Sciences, Vienna
Center for Analytical Chemistry
Department IFA-Tulln
Konrad-Lorenz-Strasse 20
3430 Tulln
Austria
and
Fondazione Edmund Mach
Research and Innovation Centre
Food Quality and Nutrition
Department
Via E. Mach 1
38010 San Michele all’Adige (TN)
Italy
Stefanie Wienkoop

University of Vienna
Department of Molecular Systems
Biology
Althanstrasse 14
1090 Vienna
Austria
Sebastian Wolf
Leibniz Institute of Plant
Biochemistry, IPB Halle
Department of Stress and
Developmental Biology
Weinberg 3
06120 Halle (Saale)
Germany