The handbook of plant metabolomics:
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| Format: | Book |
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| Language: | English |
| Published: |
Weinheim
Wiley-Blackwell
2013
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| Series: | Molecular plant biology handbook series
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| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Physical Description: | XXVI, 424 S. Ill., graph. Darst. |
| ISBN: | 9783527327775 9783527669882 |
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| 245 | 1 | 0 | |a The handbook of plant metabolomics |c ed. by Wolfram Weckwerth ... |
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IMAGE 1
V I I
CONTENTS
PREFACE XVII LIST O F CONTRIBUTORS XIX
PART I CENTRAL METABOLISM 1
1 METABOLIC PROFILING O F PLANTS BY CC-MS 3
CAMILLA B. HILL AND UTE ROESSNER 1.1 INTRODUCTION 3
1.2 METHODS A N D PROTOCOLS 7
1.2.1 SAMPLE PREPARATION 7
1.2.1.1 SAMPLING 7
1.2.1.2 HOMOGENIZATION AND EXTRACTION 7 1.2.1.3 PROCEDURE FOR POLAR
EXTRACTION O F METABOLITES 8 1.2.2 CHEMICAL DERIVATIZATION:
METHOXYMATION AND SILYLATION 9 1.2.2.1 PROCEDURE FOR THE CHEMICAL
DERIVATIZATION O F PLANT EXTRACTS 9 1.2.3 GC-MS ANALYSIS 10
1.2.3.1 PROCEDURE TO ACQUIRE GC-MS DATA 11 1.2.4 DATA PREPROCESSING A N
D EXPORT 12
1.2.4.1 PROCEDURE FOR POSTACQUISITION DATA PREPROCESSING 12 1.2.4.2 DATA
ANALYSIS AND STATISTICS 14 1.2.4.3 PROCEDURE FOR POSTACQUISITION DATA
ANALYSIS 15 1.3 APPLICATIONS O F THE TECHNOLOGY 15
1.4 PERSPECTIVES 17
REFERENCES 18
2 ISOTOPOLOGUE PROFILING - TOWARD A BETTER UNDERSTANDING O F METABOLIC
PATHWAYS 25 WOLFGANG EISENREICH, CLAUDIA HUBER, ERIKA KUTZNER, NIHAT
KNISPEL, AND NICHOLAS SCHRAMEK 2.1 INTRODUCTION 25
2.2 METHODS A N D PROTOCOLS TO DETERMINE ISOTOPOLOGUES 31 2.2.1 MASS
SPECTROMETRY 31
2.2.2 PROTOCOLS FOR ISOTOPOLOGUE PROFILING BY GC-MS 36
HTTP://D-NB.INFO/102613725X
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V I I I | CONTENTS
2.2.2.1 PROTEIN-BOUND AMINO ACIDS 36
2.2.2.2 METABOLIC INTERMEDIATES A N D POLAR PRODUCTS 37 2.2.2.3
CARBOHYDRATES 37
2.2.3 NMR SPECTROSCOPY 38
2.2.4 PROTOCOLS FOR ISOTOPOLOGUE PROFILING BY NMR 41 2.2.5 DECONVOLUTION
O F ISOTOPOLOGUE DATA 43 2.2.6 EXPANDING THE METABOLIC SPACE BY
RETROBIOSYNTHETIC ANALYSIS 45 2.3 APPLICATIONS 46
2.3.1 EXPERIMENTS USING [U- 13C6]GLUCOSE 46 2.3.2 EXPERIMENTS USING
13CC 2 4 7
2.4 PERSPECTIVES 53
REFERENCES 54
3 NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY FOR PLANT METABOLITE PROFILING
5 7 SONIA VAN DER SAR, HYE KYONG KIM, AXEL MEISSNER, ROBERT VERPOORTE,
AND YOUNG HAE CHOI 3.1 INTRODUCTION 5 7
3.2 METHODS A N D PROTOCOLS 59
3.2.1 SAMPLE PREPARATION 59
3.2.1.1 HARVESTING PLANT MATERIAL 60 3.2.1.2 DRYING 60
3.2.1.3 EXTRACTION 60
3.2.2 DATA ACQUISITION 60
3.2.3 STANDARD 1H-NMR SPECTROSCOPY 62 3.2.4 /-RESOLVED SPECTROSCOPY 62
3.2.5 DATA ANALYSIS 62
3.3 APPLICATIONS 62
3.3.1 I D 1H-NMR SPECTROSCOPY 62
3.3.2 2D NMR SPECTROSCOPY 63
3.3.2.1 /-RESOLVED SPECTROSCOPY 65 3.3.2.2 COSY A N D TOCSY 67
3.3.2.3 HMBC AND H M Q C / H S Q C 68 3.3.2.4 NOESYOR ROESY (CAMELSPIN)
69 3.3.2.5 DOSY 69
3.3.3 MAGIC ANGLE SPINNING 70
3.4 PERSPECTIVES 72
REFERENCES 72
4 COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY FOR METABOLOMICS 77
KATJA DETTMER, MARTIN F. ALMSTETTER, CHRISTIAN J. WACHSMUTH, AND PETERJ.
OEFNER
4.1 INTRODUCTION 7 7
4.2 METHODS AND PROTOCOLS 81
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CONTENTS I X
4.2.1 INSTRUMENTATION 81
4.2.2 SAMPLE PREPARATION AND ANALYSIS 8 2
4.2.3 DATA PROCESSING 83
4.2.4 METABOLIC FINGERPRINTING 83
4.2.5 QUANTITATIVE ANALYSIS O F SELECTED METABOLITES 84 4.3 APPLICATIONS
O F THE TECHNOLOGY 85
4.3.1 DATA ANALYSIS 85
4.3.2 LITERATURE 88
4.4 PERSPECTIVES 89
REFERENCES 90
5 MALDI MASS SPECTROMETRIC IMAGING O F PLANTS 93
ALES SVATOS AND HANS-PETER MOCK 5.1 INTRODUCTION 93
5.1.1 SAMPLE PREPARATION 96
5.1.2 DATA ACQUISITION 98
5.1.3 DATA PROCESSING 98
5.2 METHODS A N D PROTOCOLS 99
5.2.1 SAMPLE PREPARATION A N D HANDLING 99
5.2.1.1 INTACT TISSUES 99
5.2.1.2 CRYOSECTIONING 99
5.2.2 MATRIX DEPOSITION 100
5.2.2.1 PAINTBRUSH (FIGURE 5.2) 100 5.2.2.2 SUBLIMATION (FIGURE 5.3) 102
5.2.3 MALDI-MS IMAGING MEASUREMENT 103 5.2.3.1 BRUKER ULTRAFLEX
INSTRUMENTS 103 5.2.3.2 WATERS MALDI MICRO MX 104
5.3 IMAGING INTACT TISSUES AND OBJECTS 105
5.4 FUTURE PERSPECTIVES 109
REFERENCES 109
6 MEDICAGO TRUNCATULA ROOT AND SHOOT METABOLOMICS: PROTOCOL FOR T H E
INVESTIGATION O F T H E PRIMARY CARBON AND NITROGEN METABOLISM BASED ON
CC-MS 111 VLORA MEHMETI, LENA FRAGNER, AND STEFANIE WIENKOOP 6.1
INTRODUCTION 111
6.2 METHODS A N D PROTOCOLS 112
6.2.1 EQUIPMENT A N D SOFTWARE 112
6.2.2 BUFFERS AND CHEMICALS 112
6.2.3 PLANT MATERIAL AND HARVEST 113
6.2.4 EXTRACTION 114
6.2.5 DERIVATIZATION 115
6.2.6 GC-MS SETUP FOR THE ANALYSIS 115
6.2.7 METABOLITE IDENTIFICATION A N D QUANTIFICATION: DATA MATRIX
PROCESSING 116
IMAGE 4
X I CONTENTS
6.2.8 DATA MINING 119
6.3 APPLICATIONS O F THE TECHNOLOGY 119
6.4 PERSPECTIVES 121
REFERENCES 123
PART II SECONDARY AND LIPID METABOLISM 125
7 STUDY O F T H E VOLATILE METABOLOME IN PLANT-INSECT INTERACTIONS 127
CEORG J. F. WEINGART, NORA C. LAWO, ASTRID FORNECK, RUDOLF KRSKA, AND
RAINER SCHUHMACHER
7.1 INTRODUCTION 127
7.1.1 PLANT-INSECT INTERACTIONS 127
7.1.2 SIGNIFICANCE O F VOLATILE PLANT METABOLITES 128 7.1.3 STUDY O F
THE PLANT VOLATILE METABOLOME IN PLANT-INSECT INTERACTIONS 128 7.1.3.1
SETTING U P O F BIOLOGICAL EXPERIMENTS 129 7.1.3.2 SAMPLING, QUENCHING,
A N D SAMPLE PREPARATION 130 7.1.3.3 HEADSPACE EXTRACTION AND
MEASUREMENT BY GC-MS 131 7.1.3.4 DATA HANDLING 134
7.1.3.5 BIOLOGICAL INTERPRETATION 135 7.2 METHODS A N D PROTOCOLS 235
7.2.1 PERMANENT BREED O F INSECTS 135
7.2.2 CULTIVATION O F GRAPEVINE PLANTS AND INOCULATION WITH PHYLLOXERA
136 7.2.2.1 MATERIALS 136
7.2.2.2 PROCEDURES 136
7.2.3 SAMPLING AND QUENCHING O F PLANT TISSUE (ROOTS A N D LEAVES) 138
7.2.3.1 SAMPLING AND QUENCHING O F ROOT TIPS 138 7.2.3.2 SAMPLING AND
QUENCHING O F GRAPEVINE LEAVES 139 7.2.4 MILLING A N D WEIGHING O F
PLANT TISSUE (ROOTS A N D LEAVES) 140 7.2.4.1 MILLING AND WEIGHING O F
ROOT SAMPLES 140 7.2.4.2 MILLING AND WEIGHING O F LEAF SAMPLES 141 7.2.5
MEASUREMENT - AUTOMATED HS-SPME EXTRACTION
AND GC-MS ANALYSIS 143 7.2.5.1 MATERIALS 143
7.2.5.2 SPME METHOD 143
7.2.5.3 GC METHOD 144
7.2.5.4 MS SETTINGS 144
7.2.6 DATA PROCESSING WITH AMDIS 145
7.2.6.1 A N IN-HOUSE REFERENCE LIBRARY HAS TO B E ESTABLISHED I N
ADVANCE 145 7.2.6.2 GENERATION O F RI CALIBRATION FILE 246 7.2.6.3 BATCH
JOB ANALYSIS FOR THE SIMULTANEOUS PROCESSING O F MULTIPLE SAMPLE
CHROMATOGRAMS 146
7.2.7 STATISTICS/CHEMOMETRICS 147
7.2.7.1 UNIVARIATE STATISTICS 147 7.2.7.2 MULTIVARIATE STATISTICS 148
IMAGE 5
CONTENTS I X I
7.3 APPLICATIONS O F THE TECHNOLOGY 148
7.4 PERSPECTIVES 149
REFERENCES 150
8 METABOLOMICS IN HERBAL MEDICINE RESEARCH 155
LIE-FEN SHYUR, CHIU-PING LIU, AND SHIH-CHANG CHIEN 8.1 INTRODUCTION 155
8.2 METHODS A N D PROTOCOLS 158
8.2.1 MATERIALS 158
8.2.1.1 REAGENTS 158
8.2.1.2 EQUIPMENT 159
8.2.2 PROCEDURES 160
8.2.2.1 SAMPLE HANDLING FOR MEDICINAL PLANTS 160 8.2.2.2 SAMPLE
PREPARATION FOR LC-MS ANALYSIS 160 8.2.2.3 LC-MS ANALYSIS 161 8.2.2.4
HPLC-PHOTODIODE ARRAY (PDA) MS SETUP AND ANALYSIS 161 8.2.2.5 GC-MS
ANALYSIS 162
8.2.2.6 PLANT EXTRACT PREPARATION FOR GC-MS ANALYSIS 163 8.2.2.7 GC-MS
PARAMETERS A N D ANALYSIS 164 8.2.2.8 LC-MS A N D GC-MS DATA ANALYSIS
165 8.2.2.9 LC-SPE-NMR ANALYSIS 166 8.2.2.10 SAMPLE PREPARATION A N D
LC-SPE-NMR ANALYSIS 167 8.2.2.11 HPLC-SPE-NMR DATA ANALYSIS 168 8.3
APPLICATIONS 168
8.4 PERSPECTIVES 169
REFERENCES 170
9 INTEGRATIVE ANALYSIS O F SECONDARY METABOLISM AND TRANSCRIPT
REGULATION IN ARABIDOPSIS THALIANA 175 FUMIO MATSUDA AND KAZUKI SAITO
9.1 INTRODUCTION 175
9.2 METHODS AND PROTOCOLS 177
9.2.1 METABOLOME ANALYSIS O F PLANT SECONDARY METABOLITES 177 9.2.1.1
SAMPLE PREPARATION 177
9.2.1.2 DATA ACQUISITION 178
9.2.1.3 PREPARATION O F METABOLITE ACCUMULATION DATA FROM THE RAW
CHROMATOGRAM DATA 179 9.2.2 PREPARATION O F COMBINED DATA MATRIX 180
9.2.2.1 PREPARATION O F GENE EXPRESSION DATA 180 9.2.2.2 COMBINATION O F
DATA MATRICES 180 9.2.3 DATA MINING 180
9.2.3.1 BL-SOM ANALYSIS 180 9.2.3.2 CORRELATION ANALYSIS 181 9.2.3.3
PRINCIPAL COMPONENT ANALYSIS AND APPLICATION O F OTHER DATA MINING
TECHNIQUES 183
IMAGE 6
X I I | CONTENTS
9.3 APPLICATIONS O F THE TECHNOLOGY 183
9.4 PERSPECTIVES 187
REFERENCES 190
10 LIQUID CHROMATOGRAPHIC-MASS SPECTROMETRIC ANALYSIS OF FLAVONOIDS 197
MACIEJ STOBIECKI AND PIOTR KACHLICKI 10.1 INTRODUCTION 197
10.1.1 ROLE O F FLAVONOIDS A N D THEIR DERIVATIVES I N BIOLOGICAL
SYSTEMS 197 10.1.2 PREPARATION O F BIOLOGICAL MATERIAL FOR METABOLOMIC
ANALYSIS A N D / O R METABOLITE PROFILING 199 10.1.3 INSTRUMENTAL
CONSIDERATIONS 201
10.2 METHODS AND PROTOCOLS: LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY O F
FLAVONOIDS 206 10.2.1 GENERAL REMARKS 206
10.2.2 PLANT CULTIVATION CONDITIONS 208 10.2.3 PREPARATION O F
BIOLOGICAL MATERIAL WITH BIOTECHNOLOGICAL METHODS (CALLUS, CELL, OR
HAIRY ROOT CULTURES) 208 10.2.4 EXTRACTION O F PLANT TISSUE OR
BIOTECHNOLOGICALLY PREPARED MATERIAL 208 10.2.4.1 EXTRACTION PROCEDURE
209 10.2.5 SOLID-PHASE EXTRACTION O F CULTURE MEDIUM OR APOPLASTIC
FLUIDS 209 10.2.6 PREPARATION O F SAMPLES FOR LC-MS ANALYSES 210
10.2.7 CHROMATOGRAPHIC PROTOCOLS FOR SEPARATION O F FLAVONOID
GLYCONJUGATES 210 10.2.8 CONTROL O F IONIZATION PARAMETERS DURING MASS
SPECTROMETRIC ANALYSIS A N D IDENTIFICATION O F COMPOUNDS DURING LC-MS
METABOLITE PROFILING 211 10.3 APPLICATIONS O F THE TECHNOLOGY 211
10.4 PERSPECTIVES 211
REFERENCES 212
11 INTRODUCTION TO LIPID (FAME) ANALYSIS IN ALGAE USING CAS
CHROMATOGRAPHY-MASS SPECTROMETRY 215 TAKESHI FURUHASHI AND WOLFRAM
WECKWERTH 11.1 INTRODUCTION 215
11.2 METHODS AND EXPERIMENTAL PROTOCOL 216 11.2.1 EXTRACTION 216
11.2.2 BOUND AND FREE FATTY ACIDS 217
11.2.3 PIGMENTS 217
11.2.4 CONTAMINANTS 219
11.2.5 DERIVATIZATION 219
11.2.6 GC-MS SYSTEM 220
11.2.7 IDENTIFICATION 220
11.2.8 PROTOCOLS 221
11.2.8.1 PROTOCOL I 221
IMAGE 7
CONTENTS
1 1 . 2 . 8 . 2
11.2.9
11.3
12
12.1 12.2
12.2.1
12.2.2
12.2.3
12.2.4 12.2.5 12.2.6 12.2.7
12.2.8
12.2.9
12.2.9.1 12.2.9.2 12.2.9.3 12.2.9.4 12.2.10
12.2.10.1 12.2.10.2 12.2.10.3 12.2.11 12.3 12.4
PART III
13
13.1 13.2 13.3 13.4
PROTOCOL II 221 GC-MS INSTRUMENT A N D CONDITIONS 223 APPLICATION A N D
PERSPECTIVE 223 REFERENCES 224
MULTI-CENE TRANSFORMATION FOR PATHWAY ENGINEERING O F 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 INTRODUCTION 227 METHODS A N D
PROTOCOLS 233 CHEMICALS 233
PLASMID CONSTRUCTION O F MULTI-GENE TRANSFORMATION 233 PREPARATION O F
DUAL TERMINATOR (DT) FRAGMENT BY PCR-BASED OVERLAP EXTENSION METHOD 233
PLASMID CONSTRUCTION O F P U H R KS CSPS THSP 236 CONSTRUCTION O F P H S
G 2 9 9 CSPS 35S-CYP88-DT (FIGURE 12.2A) 236 CONSTRUCTION O F PHSG299
CSPS 35S-CYP72-DT.2 (FIGURE 12.2A) 237
CONSTRUCTION OF PHSG299-CYP93(RNAI)-DT (FIGURE 12.2A) 238 CONSTRUCTION O
F P U H R KS CSPS THSP-CYP88-CYP72-CYP93 (RNAI) 239 TRANSFORMATION O F
SOYBEAN BY PARTICLE BOMBARDMENT 239
PREPARATION O F EMBRYOGENIC SUSPENSION TISSUE CULTURE 239 PREPARATION O
F PLASMID DNA FOR PARTICLE BOMBARDMENT 240 CONDITIONS O F PARTICLE
BOMBARDMENT 240 SELECTION AND GENERATION O F TRANSGENIC SOYBEAN PLANTS
240 GC-MS ANALYSIS FOR TRITERPENE GLYCONE 241
EXTRACTION O F METABOLITE 241 ACID TREATMENT O F EXTRACTED METABOLITES
241 DERIVATIZATION O F METABOLITES 242 GC-MS CONDITIONS 242
APPLICATION O F TECHNOLOGY 242 PERSPECTIVES 243 REFERENCES 243
METABOLOMICS AND GENOMICS 245
METABOLOMICS-ASSISTED PLANT BREEDING 247 ALEXANDER HERRMANN AND NICOLAS
SCHAUER INTRODUCTION 247 METHOD 249 APPLICATIONS O F THE TECHNOLOGY 251
PERSPECTIVE 253 REFERENCES 254
IMAGE 8
CONTENTS
14 CONDUCTING GENOME-WIDE ASSOCIATION MAPPING O F METABOLITES 255
SUSANNA ATWELL AND DANIEL J. KLIEBENSTEIN 14.1 INTRODUCTION 255
14.2 METHODS A N D PROTOCOLS 256
14.2.1 BIOLOGICAL QUESTION TO BE ADDRESSED 256 14.2.2 CHEMISTRY TO STUDY
256
14.2.2.1 CHEMICAL CLASS 256 14.2.2.2 EXTRACTION AND DETECTION PLATFORM
257 14.2.3 SPECIES CHOICE 258
14.2.3.1 GENOTYPIC CHOICES 258 14.2.3.2 GWA POPULATIONS AVAILABLE 259
14.2.3.3 DOMESTICATION STATUS 260 14.2.3.4 ABILITY TO CONDUCT
APPROPRIATE FOLLOW-UP EXPERIMENTS 260 14.2.4 SHOULD I UTILIZE A N
ADDITIONAL PERTURBATION? 260 14.2.5 CONDUCTING THE PHENOTYPE
MEASUREMENTS 261 14.2.6 COMPUTATIONAL PLATFORM TO USE FOR ANALYSIS 261
14.2.6.1 SINGLE MARKER ANALYSIS 262
14.2.6.2 POPULATION STRUCTURE MODIFICATION 262 14.2.6.3 RESULTING GWA
PLOTS 262 14.2.6.4 GENE-BASED APPROACHES 263
14.2.6.5 WHAT SHOULD I USE A N D H O W DO I USE IT? 263 14.2.7 CANDIDATE
GENE SELECTION 265 14.2.8 CANDIDATE GENE VALIDATION 266 14.2.8.1
VALIDATE THAT THE GENE INFLUENCES THE PHENOTYPE? 267 14.2.8.2 VALIDATE
THAT NATURAL VARIATION I N THE GENE INFLUENCES THE
PHENOTYPE 267
14.3 APPLICATIONS 267
14.4 PERSPECTIVES 268
REFERENCES 268
PART IV METABOLOMICS AND BIOINFORMATICS 273
15 METABOLITE CLUSTERING AND VISUALIZATION O F MASS SPECTROMETRY DATA
USING ONE-DIMENSIONAL SELF-ORGANIZING MAPS 275 ALEXANDER KAEVER, MANUEL
LANDESFEIND, KIRSTIN FEUSSNER, IVO FEUSSNER, AND PETER MEINICKE 15.1
INTRODUCTION 275
15.2 METHODS A N D PROTOCOLS 276
15.2.1 DATA IMPORT 277
15.2.2 CLUSTERING 277
15.2.3 CLUSTER ANALYSIS 280
15.3 APPLICATIONS O F THE TECHNOLOGY 281
15.4 PERSPECTIVES 286
REFERENCES 286
IMAGE 9
CONTENTS X V
16 METABOLITE IDENTIFICATION AND COMPUTATIONAL MASS SPECTROMETRY 289
STEFFEN NEUMANN, FLORIAN RASCHE, SEBASTIAN WOLF, AND SEBASTIAN BOCKER
16.1 INTRODUCTION 289
16.2 ANNOTATION AND IDENTIFICATION O F METABOLITES 290 16.2.1 EXACT MASS
SEARCH I N COMPOUND LIBRARIES 291 16.2.2 DERIVING THE ELEMENTAL
COMPOSITION FROM MS 1 2 9 2 16.2.3 ELEMENTAL COMPOSITION FROM MS2 A N D
MS" 293 16.2.4 IN SILICO LIBRARY SEARCH WITH METFRAG 294 16.2.5
REFERENCE SPECTRAL LIBRARY LOOKUP 299
16.3 PERSPECTIVES 302
REFERENCES 303
17 USING COVAIN T O ANALYZE METABOLOMICS DATA 305 XIAOLIANG SUN AND
WOLFRAM WECKWERTH 17.1 INTRODUCTION 305
17.2 METHODS 308
17.2.1 DATA PREPROCESSING 308
17.2.1.1 IMPUTATION O F MISSING VALUES 308 17.2.1.2 TRANSFORMATIONS TO
SATISFY PREREQUISITES O F STATISTICAL METHODS 310 17.2.1.3 ADJUSTING
OUTLIERS 310 17.2.1.4 SCALING 310
17.2.1.5 FILTERING BY STATISTICAL FEATURES 310 17.2.2 UNI- AND BIVARIATE
STATISTICAL METHODS FOR INDIVIDUAL METABOLITE-LEVEL ANALYSIS 311
17.2.2.1 ANOVA COMPARES SINGLE METABOLITE LEVELS 311 17.2.2.2
CORRELATION COEFFICIENTS INTERPRET THE RELATIONSHIPS BETWEEN
PAIRWISE TWO METABOLITES 311 17.2.2.3 GRANGER CAUSALITY ANALYSIS
IDENTIFIES THE CAUSATION BETWEEN PAIRWISE TWO METABOLITES I N
TIME-SERIES DATA 311 17.2.3 MULTIVARIATE STATISTICAL METHODS FOR
GROUP-LEVEL ANALYSIS 312 17.2.3.1 PCA DISTINGUISHES PHENOTYPES AND FINDS
MOST INFLUENCING
METABOLITES 312
17.2.3.2 INDEPENDENT COMPONENT ANALYSIS DISTINGUISHES PHENOTYPES AND
FINDS THE LATENT SOURCES O F METABOLITES I N TIME-SERIES DATA 312
17.2.3.3 CLUSTERING CLASSIFIES DATA INTO GROUPS 312 17.2.4 NETWORK-LEVEL
ANALYSIS 313 17.2.4.1 NETWORK MAPPING 313
17.2.4.2 NETWORK INFERENCE 313 17.2.5 INFLUENCES O F DATA PREPROCESSING
O N STATISTICAL ANALYSIS RESULTS 313 17.2.5.1 O N THE MEAN VALUES:
ANOVA, CORRELATION COEFFICIENT, GRANGER ANALYSIS, AND CLUSTERING 313
17.2.5.2 O N THE VARIANCE AND COVARIANCE: ANOVA, PCA, AND ICA 314 17.3
APPLICATION 314
17.4 PERSPECTIVE 320
REFERENCES 320
IMAGE 10
CONTENTS
18 MASS SPECTRAL SEARCH AND ANALYSIS USING THE COLM METABOLOME
DATABASE 321 JAN HUMMEL, NADINE STREHMEL, CHRISTIAN BOILING, STEFANIE
SCHMIDT, DIRK WALTHER, AND JOACHIM KOPKA 18.1 INTRODUCTION 321
18.2 METHODS A N D PROTOCOLS: THE GMD A N D SUPPORTED DATA ANALYSIS
WORKFLOWS 322 18.2.1 THE GMD DATA ENTITIES 322
18.2.2 THE TEXT SEARCH QUERIES 325
18.2.3 THE MASS SPECTRUM QUERY SUBMISSION AND ANALYSIS OPTIONS 325
18.2.3.1 MASS SPECTRAL MATCHING 326 18.2.3.2 DECISION TREE
(DT)-SUPPORTED SUBSTRUCTURE PREDICTION 329 18.2.4 INTERPRETING THE MASS
SPECTRAL ANALYSIS RESULTS 329 18.2.4.1 THE MASS SPECTRAL MATCHING
RESULTS 329
18.2.4.2 THE SUBSTRUCTURE PREDICTION RESULTS 332 18.2.4.3 INTERPRETING
DECISION TREES 333 18.2.5 THE WEB SERVICES AT GMD 336
18.2.5.1 GENERAL CONSIDERATIONS 336 18.2.5.2 THE GMD WEB SERVICE MODULES
337 18.2.6 THE GMD DOWNLOAD OPTIONS 338 18.3 APPLICATIONS AND
PERSPECTIVES 341
REFERENCES 342
GLOSSARY 345
INDEX 415 |
| any_adam_object | 1 |
| building | Verbundindex |
| bvnumber | BV040918934 |
| classification_rvk | WN 1300 WN 1700 |
| ctrlnum | (OCoLC)854686490 (DE-599)BVBBV040918934 |
| discipline | Biologie |
| format | Book |
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| genre_facet | Aufsatzsammlung |
| id | DE-604.BV040918934 |
| illustrated | Illustrated |
| indexdate | 2024-08-21T00:39:44Z |
| institution | BVB |
| isbn | 9783527327775 9783527669882 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-025898120 |
| oclc_num | 854686490 |
| open_access_boolean | |
| owner | DE-11 DE-355 DE-BY-UBR DE-703 DE-20 |
| owner_facet | DE-11 DE-355 DE-BY-UBR DE-703 DE-20 |
| physical | XXVI, 424 S. Ill., graph. Darst. |
| publishDate | 2013 |
| publishDateSearch | 2013 |
| publishDateSort | 2013 |
| publisher | Wiley-Blackwell |
| record_format | marc |
| series2 | Molecular plant biology handbook series |
| spelling | The handbook of plant metabolomics ed. by Wolfram Weckwerth ... Weinheim Wiley-Blackwell 2013 XXVI, 424 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Molecular plant biology handbook series Pflanzen (DE-588)4045539-7 gnd rswk-swf Biochemische Analyse (DE-588)4255721-5 gnd rswk-swf Metabolom (DE-588)4807318-0 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Pflanzen (DE-588)4045539-7 s Metabolom (DE-588)4807318-0 s Biochemische Analyse (DE-588)4255721-5 s DE-604 Weckwerth, Wolfram Sonstige oth Erscheint auch als Online-Ausgabe, EPUB 978-3-527-66990-5 Erscheint auch als Online-Ausgabe, MOBI 978-3-527-66991-2 Erscheint auch als Online-Ausgabe, PDF 978-3-527-66989-9 X:MVB text/html http://deposit.dnb.de/cgi-bin/dokserv?id=4126132&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025898120&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | The handbook of plant metabolomics Pflanzen (DE-588)4045539-7 gnd Biochemische Analyse (DE-588)4255721-5 gnd Metabolom (DE-588)4807318-0 gnd |
| subject_GND | (DE-588)4045539-7 (DE-588)4255721-5 (DE-588)4807318-0 (DE-588)4143413-4 |
| title | The handbook of plant metabolomics |
| title_auth | The handbook of plant metabolomics |
| title_exact_search | The handbook of plant metabolomics |
| title_full | The handbook of plant metabolomics ed. by Wolfram Weckwerth ... |
| title_fullStr | The handbook of plant metabolomics ed. by Wolfram Weckwerth ... |
| title_full_unstemmed | The handbook of plant metabolomics ed. by Wolfram Weckwerth ... |
| title_short | The handbook of plant metabolomics |
| title_sort | the handbook of plant metabolomics |
| topic | Pflanzen (DE-588)4045539-7 gnd Biochemische Analyse (DE-588)4255721-5 gnd Metabolom (DE-588)4807318-0 gnd |
| topic_facet | Pflanzen Biochemische Analyse Metabolom Aufsatzsammlung |
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