Metabolome analysis: an introduction
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Hoboken, NJ
Wiley
2007
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Klappentext |
| Beschreibung: | Includes bibliographical references and index |
| Beschreibung: | XV, 311 S. Ill., graph. Darst. |
| ISBN: | 9780471743446 0471743445 |
Internformat
MARC
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| 245 | 1 | 0 | |a Metabolome analysis |b an introduction |c Silas G. Villas-Bôas ... |
| 264 | 1 | |a Hoboken, NJ |b Wiley |c 2007 | |
| 300 | |a XV, 311 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Includes bibliographical references and index | ||
| 650 | 4 | |a Génomique | |
| 650 | 4 | |a Métabolites | |
| 650 | 4 | |a Metabolites | |
| 650 | 4 | |a Genomics | |
| 650 | 0 | 7 | |a Chemische Analyse |0 (DE-588)4009840-0 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Metabolom |0 (DE-588)4807318-0 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Genanalyse |0 (DE-588)4200230-8 |2 gnd |9 rswk-swf |
| 689 | 0 | 0 | |a Metabolom |0 (DE-588)4807318-0 |D s |
| 689 | 0 | 1 | |a Chemische Analyse |0 (DE-588)4009840-0 |D s |
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| 689 | 1 | 1 | |a Genanalyse |0 (DE-588)4200230-8 |D s |
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| 700 | 1 | |a Villas-Bôas, Silas G. |e Sonstige |4 oth | |
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| 856 | 4 | 2 | |m Digitalisierung UB Bayreuth - ADAM Catalogue Enrichment |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016538024&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |3 Klappentext |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-016538024 | ||
Datensatz im Suchindex
| _version_ | 1804137713881841664 |
|---|---|
| adam_text | CONTENTS/?
PREFACE
xiii
LIST OF CONTRIBUTORS
xv
PART I: CONCEPTS AND METHODOLOGY
1
Metabolomics in Functional Genomics and Systems Biology
3
1.1
From genomic sequencing to functional genomics,
3
1.2
Systems biology and metabolic models,
6
1.3
Metabolomics,
8
1.4
Future perspectives,
11
2
The Chemical Challenge of the
Metanolomé
15
2.1
Metabolites and metabolism,
15
2.2
The structural diversity of metabolites,
18
2.2.1
The chemical and physical properties,
18
2.2.2
Metabolite abundance,
23
2.2.3
Primary and secondary metabolism,
24
2.3
The number of metabolites in a biological system,
25
2.4
Controlling rates and levels,
26
2.4.1
Control by substrate level,
27
2.4.2
Feedback and feedforward control,
27
vii
viii CONTENTS
2.4.3
Control
by pathway independent regulatory molecules,
27
2.4.4
Allosteric control,
28
2.4.5
Control by compartmentalization,
30
2.4.6
The dynamics of the metabolism
—
the mass flow,
31
2.4.7
Control by hormones,
33
2.5
Metabolic channeling or metabolons,
33
2.6
Metabolites are arranged in networks that are part of a cellular
interactome,
35
3
Sampling and Sample Preparation
39
3.1
Introduction,
39
3.2
Quenching
—
the first step,
41
3.2.1
Overview on metabolite turnover,
41
3.2.2
Different methods for quenching,
44
3.2.3
Quenching microbial and cell cultures,
44
3.2.4
Quenching plant and animal tissues,
50
3.3
Obtaining metabolites from biological samples,
52
3.3.1
Release of intracellular metabolites,
52
3.3.2
Structure of the cell envelopes—the main barrier
to be broken,
52
3.3.3
Cell disruption methods,
58
3.3.4
Nonmechanical disruption of cell envelopes,
59
3.3.5
Mechanical disruption of cell envelopes,
66
3.4
Metabolites in the extracellular medium,
71
3.4.1
Metabolites in solution,
72
3.4.2
Metabolites in the gas phase,
75
3.5
Improving detection via sample concentration,
76
4
Analytical Tools
83
4.1
Introduction,
83
4.2
Choosing a methodology,
84
4.3
Starting point
—
samples,
86
4.4
Principles of chromatography,
87
4.4.1
Basics of chromatography,
87
4.4.2
The chromatogram and terms in chromatography,
90
4.5 Chromatographie
systems,
93
4.5.1
Gas chromatography,
94
4.5.2
HPLC systems,
102
4.6
Mass spectrometry,
106
4.6.1
The mass spectrometer
—
an overview,
107
4.6.2
GC-MS—the El ion source,
109
4.6.3
LC-MS—the ESI ion source, 111
4.6.4
Mass analyzer
—
the quadrupole,
115
4.6.5
Mass analyzer
—
the ion-trap,
117
CONTENTS ix
4.6.6
Mass analyzer
—
the time-of-flight,
119
4.6.7
Detection and computing in MS,
121
4.7
The analytical work-flow,
125
4.7.1
Separation by chromatography,
125
4.7.2
Mass spectrometry,
128
4.7.3
General analytical considerations,
129
4.8
Data evaluation,
129
4.8.1
Structure of data,
129
4.8.2
The
Chromatographie
separation,
132
4.8.3
Mass spectral data,
133
4.8.4
Exporting data for processing,
135
4.9
Beyond the core methods,
136
4.9.1
Developments in chromatography,
137
4.9.2
Capillary electrophoresis,
139
4.9.3
Tandem MS and advanced scanning techniques,
141
4.9.4
NMR spectrometry,
143
4.10
Further reading,
144
5
Data Analysis
146
5.1
Organizing the data,
146
5.2
Scales of measurement,
147
5.2.1
Qualitative data,
148
5.2.2
Quantitative data,
148
5.3
Data structures,
148
5.4
Preprocessing of data,
150
5.4.1
Calibration of data,
150
5.4.2
Combining profile scans,
151
5.4.3
Filtering,
152
5.4.4
Centroid calculation,
156
5.4.5
Internal mass scale correction,
156
5.4.6
Binning,
157
5.4.7
Baseline correction,
157
5.4.8 Chromatographie
profile matching,
163
5.5
Deconvolution of
spectroscopie
data,
166
5.6
Data standardization (normalization),
167
5.7
Data transformations,
168
5.7.1
Principal component analysis,
168
5.7.2
Fisher discriminant analysis,
171
5.8
Similarities and distances between data,
173
5.8.1
Continuous functions,
173
5.8.2
Binary functions,
176
5.9
Clustering techniques,
178
5.9.1
Hierarchical clustering,
178
5.9.2
it-means clustering,
181
CONTENTS
5.10
Classification techniques,
182
5.10.1
Decision theory,
183
5.10.2
¿-nearest neighbor,
184
5.10.3
Tree-based classification,
184
5.11
Integrated tools for automation, libraries, and data evaluation,
185
PART II—CASE STUDIES AND REVIEWS
6
Yeast Metabolomics: The Discovery of New Metabolic Pathways in
Saccharomyces cerevisiae
191
6.1
Introduction,
191
6.2
Brief description of the methodology used,
192
6.2.1
Sample preparation,
192
6.2.2
The analysis,
194
6.3
Early discoveries,
194
6.4
Yeast stress response gives evidence of alternative pathway for glyoxylate
biosynthesis in S. cerevisiae,
195
6.5
Biosynthesis of glyoxylate from
glycine
in
5.
cerevisiae,
196
6.5.1
Stable isotope labeling experiment to investigate
glycine
catabolism
in S. cerevisiae,
198
6.5.2
Data leveraged for speculation,
201
7
Microbial Metabolomics: Rapid Sampling Techniques to Investigate
Intracellular Metabolite Dynamics
—
An Overview
203
7.1
Introduction,
203
7.2
Starting with a simple sampling device proposed by Theobald
et al.
(1993), 204
7.3
An improved device reported by
Lange et
al.
(2001), 205
7.4
Sampling tube device by Weuster-Botz
(1997), 207
7.5
Fully automated device by Schaefer
et al.
(1999), 209
7.6
The stopped-flow technique by Buziol
et al.
(2002), 209
7.7
The BioScope: a system for continuous-pulse experiments,
212
7.8
Conclusions and perspectives,
213
8
Plant Metabolomics
215
8.1
Introduction,
215
8.2
History of plant metabolomics,
217
8.3
Plants, their metabolism and metabolomics,
219
8.3.1
Plant structures,
219
8.3.2
Plant metabolism,
222
8.4
Specific challenges in plant metabolomics,
223
8.4.1
Light dependency of plant metabolism,
223
CONTENTS
Xi
8.4.2
Extraction of plant metabolites,
225
8.4.3
Many cell types in one tissue,
225
8.4.4
The dynamical range of plant metabolites,
226
8.4.5
Complexity of the plant metabolome,
226
8.4.6
Development of databases for metabolomics-derived data in plant
science,
228
8.5
Applications of metabolomics approaches in plant research,
229
8.5.1
Phenotyping,
229
8.5.2
Functional genomics,
231
8.5.3
Fluxomics,
232
8.5.4
Metabolic trait analysis,
232
8.5.5
Systems biology,
234
8.6
Future perspectives,
234
9
Mass Profiling of Fungal Extract from
Pénicillium
Species
239
9.1
Introduction,
239
9.2
Methodology for screening of fungi by DiMS,
242
9.2.1
Cultures,
243
9.2.2
Extraction,
243
9.2.3
Analysis by direct infusion mass spectrometry,
244
9.3
Discussion,
245
9.3.1
Initial data processing,
245
9.3.2
Metabolite prediction,
246
9.3.3
Chemical diversity and similarity,
248
9.4
Conclusion,
252
10
Metabolomics in Humans and Other Mammals
253
10.1
Introduction,
253
10.2
A brief history of mammalian metabolomics,
257
10.3
Sample preparation for mammalian metabolomics studies,
260
10.3.1
Working with blood,
262
10.3.2
Working with urine,
263
10.3.3
Working with
cerebrospinal
fluid,
264
10.3.4
Working with cells and tissues,
267
10.4
Sample analysis,
268
10.4.1
GC-MS analysis of urine, plasma, and CSF,
269
10.4.2
LC-MS analysis of urine, blood, and CFS,
271
10.4.3
NMR analysis of CSF, urine, and blood,
274
10.5
Applications,
277
10.5.1
Identification and classification of metabolic disorders,
278
10.6
Future outlook,
283
INDEX
289
A concise, interdisciplinary
introduction to metabolome analysis
•
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ι
itabos
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|
| adam_txt |
CONTENTS/?
PREFACE
xiii
LIST OF CONTRIBUTORS
xv
PART I: CONCEPTS AND METHODOLOGY
1
Metabolomics in Functional Genomics and Systems Biology
3
1.1
From genomic sequencing to functional genomics,
3
1.2
Systems biology and metabolic models,
6
1.3
Metabolomics,
8
1.4
Future perspectives,
11
2
The Chemical Challenge of the
Metanolomé
15
2.1
Metabolites and metabolism,
15
2.2
The structural diversity of metabolites,
18
2.2.1
The chemical and physical properties,
18
2.2.2
Metabolite abundance,
23
2.2.3
Primary and secondary metabolism,
24
2.3
The number of metabolites in a biological system,
25
2.4
Controlling rates and levels,
26
2.4.1
Control by substrate level,
27
2.4.2
Feedback and feedforward control,
27
vii
viii CONTENTS
2.4.3
Control
by "pathway independent" regulatory molecules,
27
2.4.4
Allosteric control,
28
2.4.5
Control by compartmentalization,
30
2.4.6
The dynamics of the metabolism
—
the mass flow,
31
2.4.7
Control by hormones,
33
2.5
Metabolic channeling or metabolons,
33
2.6
Metabolites are arranged in networks that are part of a cellular
interactome,
35
3
Sampling and Sample Preparation
39
3.1
Introduction,
39
3.2
Quenching
—
the first step,
41
3.2.1
Overview on metabolite turnover,
41
3.2.2
Different methods for quenching,
44
3.2.3
Quenching microbial and cell cultures,
44
3.2.4
Quenching plant and animal tissues,
50
3.3
Obtaining metabolites from biological samples,
52
3.3.1
Release of intracellular metabolites,
52
3.3.2
Structure of the cell envelopes—the main barrier
to be broken,
52
3.3.3
Cell disruption methods,
58
3.3.4
Nonmechanical disruption of cell envelopes,
59
3.3.5
Mechanical disruption of cell envelopes,
66
3.4
Metabolites in the extracellular medium,
71
3.4.1
Metabolites in solution,
72
3.4.2
Metabolites in the gas phase,
75
3.5
Improving detection via sample concentration,
76
4
Analytical Tools
83
4.1
Introduction,
83
4.2
Choosing a methodology,
84
4.3
Starting point
—
samples,
86
4.4
Principles of chromatography,
87
4.4.1
Basics of chromatography,
87
4.4.2
The chromatogram and terms in chromatography,
90
4.5 Chromatographie
systems,
93
4.5.1
Gas chromatography,
94
4.5.2
HPLC systems,
102
4.6
Mass spectrometry,
106
4.6.1
The mass spectrometer
—
an overview,
107
4.6.2
GC-MS—the El ion source,
109
4.6.3
LC-MS—the ESI ion source, 111
4.6.4
Mass analyzer
—
the quadrupole,
115
4.6.5
Mass analyzer
—
the ion-trap,
117
CONTENTS ix
4.6.6
Mass analyzer
—
the time-of-flight,
119
4.6.7
Detection and computing in MS,
121
4.7
The analytical work-flow,
125
4.7.1
Separation by chromatography,
125
4.7.2
Mass spectrometry,
128
4.7.3
General analytical considerations,
129
4.8
Data evaluation,
129
4.8.1
Structure of data,
129
4.8.2
The
Chromatographie
separation,
132
4.8.3
Mass spectral data,
133
4.8.4
Exporting data for processing,
135
4.9
Beyond the core methods,
136
4.9.1
Developments in chromatography,
137
4.9.2
Capillary electrophoresis,
139
4.9.3
Tandem MS and advanced scanning techniques,
141
4.9.4
NMR spectrometry,
143
4.10
Further reading,
144
5
Data Analysis
146
5.1
Organizing the data,
146
5.2
Scales of measurement,
147
5.2.1
Qualitative data,
148
5.2.2
Quantitative data,
148
5.3
Data structures,
148
5.4
Preprocessing of data,
150
5.4.1
Calibration of data,
150
5.4.2
Combining profile scans,
151
5.4.3
Filtering,
152
5.4.4
Centroid calculation,
156
5.4.5
Internal mass scale correction,
156
5.4.6
Binning,
157
5.4.7
Baseline correction,
157
5.4.8 Chromatographie
profile matching,
163
5.5
Deconvolution of
spectroscopie
data,
166
5.6
Data standardization (normalization),
167
5.7
Data transformations,
168
5.7.1
Principal component analysis,
168
5.7.2
Fisher discriminant analysis,
171
5.8
Similarities and distances between data,
173
5.8.1
Continuous functions,
173
5.8.2
Binary functions,
176
5.9
Clustering techniques,
178
5.9.1
Hierarchical clustering,
178
5.9.2
it-means clustering,
181
CONTENTS
5.10
Classification techniques,
182
5.10.1
Decision theory,
183
5.10.2
¿-nearest neighbor,
184
5.10.3
Tree-based classification,
184
5.11
Integrated tools for automation, libraries, and data evaluation,
185
PART II—CASE STUDIES AND REVIEWS
6
Yeast Metabolomics: The Discovery of New Metabolic Pathways in
Saccharomyces cerevisiae
191
6.1
Introduction,
191
6.2
Brief description of the methodology used,
192
6.2.1
Sample preparation,
192
6.2.2
The analysis,
194
6.3
Early discoveries,
194
6.4
Yeast stress response gives evidence of alternative pathway for glyoxylate
biosynthesis in S. cerevisiae,
195
6.5
Biosynthesis of glyoxylate from
glycine
in
5.
cerevisiae,
196
6.5.1
Stable isotope labeling experiment to investigate
glycine
catabolism
in S. cerevisiae,
198
6.5.2
Data leveraged for speculation,
201
7
Microbial Metabolomics: Rapid Sampling Techniques to Investigate
Intracellular Metabolite Dynamics
—
An Overview
203
7.1
Introduction,
203
7.2
Starting with a simple sampling device proposed by Theobald
et al.
(1993), 204
7.3
An improved device reported by
Lange et
al.
(2001), 205
7.4
Sampling tube device by Weuster-Botz
(1997), 207
7.5
Fully automated device by Schaefer
et al.
(1999), 209
7.6
The stopped-flow technique by Buziol
et al.
(2002), 209
7.7
The BioScope: a system for continuous-pulse experiments,
212
7.8
Conclusions and perspectives,
213
8
Plant Metabolomics
215
8.1
Introduction,
215
8.2
History of plant metabolomics,
217
8.3
Plants, their metabolism and metabolomics,
219
8.3.1
Plant structures,
219
8.3.2
Plant metabolism,
222
8.4
Specific challenges in plant metabolomics,
223
8.4.1
Light dependency of plant metabolism,
223
CONTENTS
Xi
8.4.2
Extraction of plant metabolites,
225
8.4.3
Many cell types in one tissue,
225
8.4.4
The dynamical range of plant metabolites,
226
8.4.5
Complexity of the plant metabolome,
226
8.4.6
Development of databases for metabolomics-derived data in plant
science,
228
8.5
Applications of metabolomics approaches in plant research,
229
8.5.1
Phenotyping,
229
8.5.2
Functional genomics,
231
8.5.3
Fluxomics,
232
8.5.4
Metabolic trait analysis,
232
8.5.5
Systems biology,
234
8.6
Future perspectives,
234
9
Mass Profiling of Fungal Extract from
Pénicillium
Species
239
9.1
Introduction,
239
9.2
Methodology for screening of fungi by DiMS,
242
9.2.1
Cultures,
243
9.2.2
Extraction,
243
9.2.3
Analysis by direct infusion mass spectrometry,
244
9.3
Discussion,
245
9.3.1
Initial data processing,
245
9.3.2
Metabolite prediction,
246
9.3.3
Chemical diversity and similarity,
248
9.4
Conclusion,
252
10
Metabolomics in Humans and Other Mammals
253
10.1
Introduction,
253
10.2
A brief history of mammalian metabolomics,
257
10.3
Sample preparation for mammalian metabolomics studies,
260
10.3.1
Working with blood,
262
10.3.2
Working with urine,
263
10.3.3
Working with
cerebrospinal
fluid,
264
10.3.4
Working with cells and tissues,
267
10.4
Sample analysis,
268
10.4.1
GC-MS analysis of urine, plasma, and CSF,
269
10.4.2
LC-MS analysis of urine, blood, and CFS,
271
10.4.3
NMR analysis of CSF, urine, and blood,
274
10.5
Applications,
277
10.5.1
Identification and classification of metabolic disorders,
278
10.6
Future outlook,
283
INDEX
289
A concise, interdisciplinary
introduction to metabolome analysis
•
ІП
!
■
>ien
d
ι
narr
:s
oř
biochemical
ι
itabos
methodoio
sample preparation,
5
dentificaî
ìl
tools
(і
-e appi:
sanddis·
peču!
requiremet
таіп
gì
inísm
cessft ìbolome
■
■
metabołom
ι
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MICHAEL A. E.
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| dewey-full | 572.8/6 |
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| discipline | Biologie Chemie |
| discipline_str_mv | Biologie Chemie |
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| id | DE-604.BV023354463 |
| illustrated | Illustrated |
| index_date | 2024-07-02T21:06:27Z |
| indexdate | 2024-07-09T21:16:40Z |
| institution | BVB |
| isbn | 9780471743446 0471743445 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016538024 |
| oclc_num | 70291995 |
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| physical | XV, 311 S. Ill., graph. Darst. |
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| spelling | Metabolome analysis an introduction Silas G. Villas-Bôas ... Hoboken, NJ Wiley 2007 XV, 311 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Génomique Métabolites Metabolites Genomics Chemische Analyse (DE-588)4009840-0 gnd rswk-swf Metabolom (DE-588)4807318-0 gnd rswk-swf Genanalyse (DE-588)4200230-8 gnd rswk-swf Metabolom (DE-588)4807318-0 s Chemische Analyse (DE-588)4009840-0 s DE-604 Genanalyse (DE-588)4200230-8 s Villas-Bôas, Silas G. Sonstige oth Digitalisierung UB Bayreuth - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016538024&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Bayreuth - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016538024&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext |
| spellingShingle | Metabolome analysis an introduction Génomique Métabolites Metabolites Genomics Chemische Analyse (DE-588)4009840-0 gnd Metabolom (DE-588)4807318-0 gnd Genanalyse (DE-588)4200230-8 gnd |
| subject_GND | (DE-588)4009840-0 (DE-588)4807318-0 (DE-588)4200230-8 |
| title | Metabolome analysis an introduction |
| title_auth | Metabolome analysis an introduction |
| title_exact_search | Metabolome analysis an introduction |
| title_exact_search_txtP | Metabolome analysis an introduction |
| title_full | Metabolome analysis an introduction Silas G. Villas-Bôas ... |
| title_fullStr | Metabolome analysis an introduction Silas G. Villas-Bôas ... |
| title_full_unstemmed | Metabolome analysis an introduction Silas G. Villas-Bôas ... |
| title_short | Metabolome analysis |
| title_sort | metabolome analysis an introduction |
| title_sub | an introduction |
| topic | Génomique Métabolites Metabolites Genomics Chemische Analyse (DE-588)4009840-0 gnd Metabolom (DE-588)4807318-0 gnd Genanalyse (DE-588)4200230-8 gnd |
| topic_facet | Génomique Métabolites Metabolites Genomics Chemische Analyse Metabolom Genanalyse |
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