Proteome research: concepts, technology and application ; with 16 tables
Gespeichert in:
| Format: | Elektronisch E-Book |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2007
|
| Ausgabe: | 2. ed. |
| Schriftenreihe: | Principles and practice
|
| Schlagworte: | |
| Online-Zugang: | UBR01 Volltext Inhaltsverzeichnis |
| Beschreibung: | 1 Online-Ressource |
| ISBN: | 9783540712404 9783540729105 |
| DOI: | 10.1007/978-3-540-72910-5 |
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| 245 | 1 | 0 | |a Proteome research |b concepts, technology and application ; with 16 tables |c M. R. Wilkins ... (eds.) |
| 250 | |a 2. ed. | ||
| 264 | 1 | |a Berlin [u.a.] |b Springer |c 2007 | |
| 300 | |a 1 Online-Ressource | ||
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| 700 | 1 | |a Wilkins, Marc R. |e Sonstige |4 oth | |
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Datensatz im Suchindex
| _version_ | 1804137240012521472 |
|---|---|
| adam_text | 1 TEN YEARS OF TH
E PROTEOM
E 1
MARC
R.
WILKINS AND RON
D.
APPEL
1.1 INTRODUCTION TO THE PROTEOME 1
1.1.1 WHAT
S IN A WORD? 2
1.1.2 COULD THINGS HAVE BEEN DIFFERENT? 3
1.2 PROTEORNICS IS TECHNOLOGY-DRIVEN 3
1.2.1 PROTEIN SEPARATIONS 3
1.2.2 MASS SPECTROMETRY 5
1.2.3 MAKING SENSE OF ALL THE DATA 6
1.3 WHAT HAS PROTEOMICS DELIVERED? 8
1.4 WHAT STILL ELUDES US? 9
1.5 THIS BOOK AN
D SOME CONCLUSIONS 11
REFERENCES 11
2 SAMPLE PREPARATION AND PREFRACTIONATION TECHNIQUES
FOR ELECTROPHORESIS-BASED PROTEOMICS 15
BEN
R.
HERBERT, PIER GIORGIO RIGHETTI, ATTILIO CITTERIO, AND EGISTO BOSCHETTI
2.1 INTRODUCTION 15
2.2 CONVENTIONAL SAMPLE PREPARATION 16
2.3 ARTEFACTS 18
2.3.1 CYSTEINE CHEMISTRY - REDUCTION AND ALKYLATION 18
2.3.2 CYSTEINE CHEMISTRY - (3-ELIMINATION 19
2.3.3 LYSINE CHEMISTRY - CARBAMYLATION 20
2.4 MULTIPLEXED APPROACHES TO PROTEOMICS 22
2.5 PREFRACTIONATION TOOLS 24
2.5.1 FRACTIONAL CENTRIFUGATION 24
2.5.2 CHROMATOGRAPHIC TECHNIQUES 25
2.5.2.1 GENERAL CHROMATOGRAPHIC METHODS 25
2.5.2.2 SAMPLE FRACTIONATION WITH STACKED SORBENTS 26
2.5.3 ELECTROPHORESIS-BASED METHODS 26
2.5.3.1 CONTINUOUS ELECTROPHORESIS IN FREE LIQUID FILMS 27
2.5.3.2 ROTATIONALLY STABILISED FOCUSING APPARATUS:
THE ROTOFOR 28
2.5.3.3 SAMPLE PREFRACTIONATION VIA MULTICOMPARTMENT
ELECTROLYSERS WITH ISOELECTRIC MEMBRANES 28
2.5.3.4 MINIATURISED ISOELECTRIC SEPARATION DEVICES 30
2.6 OTHER METHODS FOR PREFRACTIONATION OF SAMPLES 30
XVIII CONTENTS
2.6.1 DEPLETIO
N O
F HIGH-ABUNDANC
E PROTEIN
S .....................
. 3
0
2.6.2 EQUALISE
R BEADS
: TH
E DEMOCRATI
C VERSU
S
TH
E PLUTOCRATI
C PROTEOM
E .................................
. 3.1
2.7 CONCLUSION
S 35
REFERENCES .3
6
3 PROTEI
N IDENTIFICATIO
N I
N PROTEOMIC
S ...................................
. 4
1
PATRICIA HERNANDEZ, PIERRE-ALAIN BINZ, AND MAR
C
R.
WILKINS
3.1 INTRODUCTIO
N 41
3.2 ATTRIBUTE
S OF PROTEIN
S USEFUL FOR THEI
R IDENTIFICATIO
N . 42
3.2.1 SPECIE
S OF ORIGI
N 42
3.2.2 PROTEI
N ISOELECTRI
C POIN
T 4
2
3.2.3 PROTEI
N MASS 42
3.2.4 PARTIA
L SEQUENC
E O
R SEQUENC
E TA
G 4
3
3.2.5 PROTEI
N AMIN
O ACI
D COMPOSITIO
N 4
3
3.3 PROTEI
N IDENTIFICATIO
N B
Y MAS
S SPECTROMETR
Y 4
5
3.3.1 TOP-DOWN
VERSU
S BOTTOM-UP
STRATEGIE
S FOR PROTEI
N
IDENTIFICATIO
N 4
5
3.3.2 INTRODUCTIO
N T
O MAS
S SPECTROMETR
Y 4
7
3.3.2.1 IONISATIO
N 47
3.3.2.2 MASS ANALYSI
S 48
3.3.2.3 INSTRUMENTATIO
N 5
0
3.3.3 PROTEI
N IDENTIFICATIO
N B
Y PEPTID
E MAS
S FINGERPRINTIN
G 5
1
3.3.3.1 PRINCIPL
E 51
3.3.3.2 IDENTIFICATIO
N AN
D CHARACTERISATIO
N O
F MODIFIE
D
PEPTIDE
S B
Y PEPTID
E MAS
S FINGERPRINTIN
G 5
3
3.3.3.3 LIMITATION
S O
F PEPTID
E MAS
S FINGERPRINTIN
G 5
5
3.3.4 TANDE
M MASS SPECTROMETR
Y BASE
D IDENTIFICATIO
N 5
6
3.3.4.1 TANDE
M MAS
S SPECTROMETR
Y SPECTR
A 5
6
3.3.4.2 THE PEPTID
E FRAGMEN
T FINGERPRINTING
APPROAC
H 5
7
3.3.4.3 DE NOV
O SEQUENCIN
G 60
3.3.4.4 IDENTIFICATIO
N AN
D CHARACTERISATIO
N O
F PEPTIDE
S
WIT
H UNEXPECTE
D MODIFICATION
S 6
1
3.3.4.5 SPECTRA
L LIBRAR
Y SEARCHE
S 62
3.4 LIST OF TOOL
S AN
D URLS 65
3.5 CONCLUDIN
G REMARK
S 65
REFERENCES 66
4 QUANTITATIO
N IN PROTEOMIC
S 69
GARRY
L.
CORTHALS AND KEITH ROSE
4.1 INTRODUCTION 69
4.2 NON-MASS-SPECTROMETRIC APPROACHES TO QUANTITATION 70
4.3 RELATIVE QUANTITATION BY MASS SPECTROMETRY 74
4.3.1 ABSOLUTE OR RELATIVE QUANTITATION? 76
4.3.2 INTRODUCTION OF STABLE ISOTOPES USING CHEMICAL TAGS 76
4.3.3 ENZYME-MEDIATED INCORPORATION OF STABLE ISOTOPES 80
4.3.4 BIOLOGICAL INCORPORATION OF STABLE ISOTOPES
BY METABOLIC LABELLING 81
CONTENTS XIX
4.3.
5 RELATIV
E QUANTISATIO
N WITHOU
T US
E O
F STABL
E
ISOTOP
E LABELLIN
G ......................................
. 8
2
4.3.
6 ABSOLUT
E QUANTITATIO
N B
Y MAS
S SPECTROMETR
Y ...............
. 8
2
4.
4 ANALYSI
S O
F KNOW
N POST-TRANSLATIONA
L MODIFICATION
S ...............
. 8
3
4.4.
1 GLYCOSYLATION..........................................
. 8
3
4.4.2
PHOSPHORYLATION 85
4.4.3
UBIQUITINYLATION 87
4.5 CONCLUSIONS 87
REFERENCES 88
5 ONE GENE, MANY PROTEIN
S 95
NICOLLE
H.
PACKER, ANDREW
A.
GOOLEY, AND MARC
R.
WILKINS
5.1 INTRODUCTION 95
5.2 AN OVERVIEW OF MODIFICATIONS: WHAT ARE THEY AN
D WHERE
DO THEY OCCUR? 99
5.3 HOW DO WE FIND POST-TRANSLATIONAL MODIFICATIONS? 100
5.3.1 SEPARATION OF ISOFORMS 100
5.3.2 DETECTION OF CO- AND POST-TRANSLATIONAL MODIFICATIONS 102
5.3.3 STRATEGY FOR THE ANALYSIS OF MODIFICATIONS:
TOP DOWN VERSUS BOTTOM UP 103
5.3.4 MASS SPECTROMETRY FOR ANALYSIS OF CO- AN
D
POST-TRANSLATIONAL MODIFICATIONS 104
5.4 ANALYSIS OF SPECIFIC MODIFICATIONS 105
5.4.1 ACETYLATION 106
5.4.2 PHOSPHORYLATION 106
5.4.3 UBIQUITINATION AND SUMOYLATION 107
5.4.4 GLYCOSYLATION 107
5.5 THE FUNCTION OF PROTEIN POST-TRANSLATIONAL MODIFICATIONS:
MORE THAN MEETS THE EYE? 109
5.6 SOME INTERESTING MODIFICATION STORIES IL
L
5.6.1 THE ERYTHROPOIETIN STORY IL
L
5.6.2 THE APOLIPOPROTEIN E STORY 113
5.6.3 THE PROGERIA STORY 114
5.6.4 THE INFLUENZA STORY 115
5.7 FUTURE DIRECTIONS 116
REFERENCES 116
6 PROTEOME IMAGING 123
PATRICIA
M.
PALAGI, DANIEL WALTHER, CATHERINE
G.
ZIMMERMANN-IVOL,
AND RON
D.
APPEL
6.1 INTRODUCTION 123
6.2 IMAGE ANALYSIS OF TWO-DIMENSIONAL ELECTROPHORESIS GELS 124
6.2.1 FIRST STEPS IN GEL IMAGE ANALYSIS 125
6.2.2 APPLICATIONS TO DIFFERENT PROTEOMICS APPROACHES 127
6.2.2.1 SINGLE-GEL ANALYSIS 128
6.2.2.2 GROUPS OF GELS 128
6.2.2.3 TWO-DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS 128
XX CONTENTS
6.
3 LIQUI
D CHROMATOGRAPHY-MAS
S SPECTROMETR
Y .....................
. 130
6.3.1 FIRS
T STEP
S I
N LIQUI
D CHROMATOGRAPHY-MAS
S
SPECTROMETR
Y IMAG
E ANALYSI
S ............................
. 130
6.3.2 APPLICATION
S T
O DIFFEREN
T PROTEOMIC
S APPROACHE
S ............13
1
6.3.2.
1 MONITORIN
G EXPERIMENT
S AN
D POST-TRANSLATIONA
L
MODIFICATION
S ..................................
. 131
6.3.2.
2 SAMPL
E POPULATION
S .............................
. 132
6.
4 TH
E MOLECULA
R SCANNE
R .......................................
. 134
6.
5 IMAGIN
G MAS
S SPECTROMETR
Y ...................................
. 138
6.5.1 IMAGIN
G MAS
S SPECTROMETR
Y - TECHNICA
L ASPECT
S 13
9
6.5.2 IMAGIN
G MAS
S SPECTROMETR
Y - APPLICATION
S 140
6.
6 CONCLUSIO
N 141
REFERENCE
S 142
7 DAT
A INTEGRATIO
N I
N PROTEOMIC
S 145
FREDERIQUE LISACEK, CHRISTINE HOOGLAND, LYDIE BOUGUELERET, AND AMOS
BAIROCH
7.1 INTRODUCTION 145
7.2 INTEGRATION AS GATHERING AND CROSS-LINKING INFORMATION 148
7.2.1 SELECTION OF SOURCES AN
D QUANTIFICATION 148
7.2.1.1 TRENDS IN DATABASES 148
7.2.1.2 DATA EVOLUTION 149
7.2.2 BIOLOGY INSPIRED CROSS-LINKING 150
7.2.2.1 THE UNIPROT UNIVERSAL PROTEIN KNOWLEDGEBASE 150
7.2.2.2 HUMAN PROTEI
N ATLAS 152
7.2.3 INTEGRATING ELEMENTS OF THE PROTEOMICS WORKFLOW 153
7.2.3.1 HIGH-THROUGHPUT DATA: STANDARDS AND REPOSITORIES ..
. 153
7.2.3.2 SWISS-2DPAGE 154
7.2.3.3 PEPTIDEATLAS AN
D THE GLOBAL PROTEOME MACHINE 155
7.2.3.4 OTHER NOTEWORTHY EFFORTS 156
7.2.4 INTEGRATION AS A FEDERATED EFFORT 156
7.2A.I
PROTEOMICS SERVERS 156
7.2.4.2 SEMANTIC WEB APPROACH 158
7.3 INTEGRATION AS BLENDING OF INFORMATION 159
7.3.1 TEXTUAL INFORMATION 159
7.3.2 ONTOLOGIES 160
7.3.3 EXAMPLES OF VISUALISATION TOOLS MERGING SEVERAL SOURCES 161
7.3.4 FROM DATA INTEGRATION TO SYSTEMS BIOLOGY 162
7.4 CONCLUDING REMARKS 164
REFERENCES 164
8 PROTEIN-PROTEIN INTERACTIONS 169
ANNE-CLAUDE GAVIN
8.1 INTRODUCTION 169
8.2 PROTEIN-PROTEI
N INTERACTIONS IN HUMAN DISEASES: ALTERED PROTEIN
CONNECTIVITY LEADS TO DISORDER 170
8.3 CHARTING PROTEIN-PROTEI
N INTERACTIONS 172
8.3.1 CHARACTERISATION OF ALL CODING SEQUENCES
IN AN ORGANISM 175
CONTENT
S XXI.
8.3.
2 MONITORIN
G BINAR
Y INTERACTIONS
: TH
E YEAS
T
TWO-HYBRI
D SYSTE
M 17
5
8.3.
3 ANALYSI
S O
F PROTEI
N COMPLEXE
S B
Y AFFINIT
Y PURIFICATIO
N
AN
D MAS
S SPECTROMETR
Y .................................
. 17
7
8.3.
4 LUMINESCENCE-BASE
D MAMMALIA
N INTERACTOM
E MAPPIN
G ......
. 18
0
8.3.
5 PROTEI
N MICROARRAY
S 18
0
8.3.
6 DAT
A QUALIT
Y 18
0
8.4 BIOLOGICA
L AN
D BIOMEDICA
L APPLICATION
S . 18
1
8.4.
1 CHARTIN
G O
F
DISEASE
S AN
D
PHARMACOLOGICALL
Y
RELEVAN
T
PATHWAY
S
18
1
8.4.
2
LESSON
S LEARNE
D FRO
M GLOBA
L
INTERACTIO
N ANALYSE
S I
N YEAS
T ...
. 18
2
8.4.
3
A
N
EMERGIN
G APPLICATION
: TH
E DEVELOPMEN
T
O
F SMALL-MOLECUL
E PROTEIN-PROTEI
N INTERACTIO
N INHIBITOR
S .....
. 18
4
8.5 FUTUR
E DIRECTION
S 186
REFERENCE
S 18
7
9 BIOMEDICA
L APPLICATION
S O
F PROTEOMIC
S 19
3
JEAN-CHARLES SANCHEZ,
YOHANN
COUTE,
LAURE
ALLARD,
PIERRE LESCUYER, AND DENI
S
F.
HOCHSTRASSER
9.1 INTRODUCTIO
N 193
9.2 THE APPLICATION OF PROTEOMIC
S TO MEDICIN
E 194
9.3 DISEAS
E DIAGNOSIS FROM BODY FLUIDS 196
9.4 VASCULAR DISEASES 197
9.4.1 INTRODUCTION 197
9.4.2 APPLICATION OF PROTEOMICS TO VASCULAR DISEASE
S
AND ATHEROSCLEROSIS 198
9.4.3 APPLICATION OF PROTEOMICS TO CARDIOVASCULAR DISEASE
S 199
9.4.4 APPLICATION OF PROTEOMICS TO CEREBROVASCULAR DISEASE 200
9.4.5 CONCLUSION 201
9.5 NEURODEGENERATIVE DISORDERS 202
9.5.1 BRAIN PROTEOM
E 202
9.5.2 PROTEOMIC PROFILING OF NEURODEGENERATIV
E DISORDER
S 203
9.5.3 CEREBROSPINAL FLUID PROTEIN MARKERS 205
9.6 PROTEOMIC
S AND CANCER 206
9.6.1 BIOMARKER DISCOVER
Y IN CANCER PROTEOMIC
S 207
9.6.1.1 TISSUE
S 207
9.6.1.2 PRIMARY AND ESTABLISHED CELL LINES 208
9.6.2 PROTEOMIC PROFILING IN ONCOLOG
Y 209
9.6.2.1 SURFACE-ENHANCED LASER DESORPTION/IONISATIO
N
TIME-OF-FLIGHT MASS SPECTROMETRY .....21
0
9.6.2.2 PROTEIN MICROARRAYS 210
9.6.2.3 TISSU
E PROFILING BY MATRIX-ASSISTED LASER
DESOPRTIOON/IONISATIO
N MASS SPECTROMETRY IMAGING .
. 210
9.6.3 USE OF PROTEOMIC
S TO DEFINE THE TISSUE OF ORIGIN 211
9.6.4 CONCLUSION 211
9.7 TOXICOPHARMACOLOGY
: THE EXAMPLE OF TYPE 2 DIABETE
S 211
9.7.1 INTRODUCTION TO DIABETES 212
9.7.2 PATHOGENESIS OF TYPE 2 DIABETE
S 212
XXII CONTENTS
9.7.3 TREATMENT
S O
F TYP
E 2 DIABETE
S ........................
. 21
3
9.7.4 PROTEOMIC
S FOR TH
E DISCOVER
Y O
F TREATMEN
T TARGET
S
FOR TYPE 2 DIABETE
S ..................................
. 21
3
9.8 CURREN
T LIMITATION
S AN
D FUTUR
E DIRECTION
S O
F PROTEOMIC
S
FOR MEDICIN
E 215
9.8.1 PREANALYTICA
I ISSUE
S ......................21
5
9.8.2 ANALYTICA
L ASPECT
S 216
9.8.3 POSTANALYTICA
L ASPECT
S 21
7
9.9 PRESEN
T AN
D FUTUR
E DIRECTION
S 217
REFERENCE
S 21
7
10 PROTEOMICS
: WHERE TO NEXT?
.
22
3
KEITH
L.
WILLIAMS AND DENIS
F.
HOCHSTRASSER
10.1 INTRODUCTIO
N 223
10.2 THE RELEVANCE OF -OMIC
S TO BIOLOGY 22
4
10.3 TECHNOLOGICA
L DEVELOPMENT
S IN PROTEOMIC
S 22
5
10.3.1 CHARACTERISING MODIFICATIONS 226
10.3.2 GLOBAL TISSUE ANALYSI
S 226
10.4 THE NEX
T STEPS FOR PROTEOMICS
: DIAGNOSTIC
S AN
D DRUGS 22
7
10.4.1 DIAGNOSTIC
S 228
10.4.2 DRUG
S 228
10.5 CONCLUSION
S 229
REFERENCES 229
INDE
X 231
PPN: 265755956
TITEL: PROTEOME RESEARCH : CONCEPTS, TECHNOLOGY AND APPLICATION / M. R.
WILKINS ... (EDS.). - . -
BERLIN : SPRINGER, 2007
ISBN: 978-3-540-71240-4GB.EUR 149.75 (FREIER PR.), SFR 229.50 (FREIER
PR.); 3-540-71240
2GB.EUR 149.75 (FREIER PR.), SFR 229.50 (FREIER PR.)
BIBLIOGRAPHISCHER DATENSATZ IM SWB-VERBUND
|
| adam_txt |
1 TEN YEARS OF TH
E PROTEOM
E 1
MARC
R.
WILKINS AND RON
D.
APPEL
1.1 INTRODUCTION TO THE PROTEOME 1
1.1.1 WHAT'
S IN A WORD? 2
1.1.2 COULD THINGS HAVE BEEN DIFFERENT? 3
1.2 PROTEORNICS IS TECHNOLOGY-DRIVEN 3
1.2.1 PROTEIN SEPARATIONS 3
1.2.2 MASS SPECTROMETRY 5
1.2.3 MAKING SENSE OF ALL THE DATA 6
1.3 WHAT HAS PROTEOMICS DELIVERED? 8
1.4 WHAT STILL ELUDES US? 9
1.5 THIS BOOK AN
D SOME CONCLUSIONS 11
REFERENCES 11
2 SAMPLE PREPARATION AND PREFRACTIONATION TECHNIQUES
FOR ELECTROPHORESIS-BASED PROTEOMICS 15
BEN
R.
HERBERT, PIER GIORGIO RIGHETTI, ATTILIO CITTERIO, AND EGISTO BOSCHETTI
2.1 INTRODUCTION 15
2.2 CONVENTIONAL SAMPLE PREPARATION 16
2.3 ARTEFACTS 18
2.3.1 CYSTEINE CHEMISTRY - REDUCTION AND ALKYLATION 18
2.3.2 CYSTEINE CHEMISTRY - (3-ELIMINATION 19
2.3.3 LYSINE CHEMISTRY - CARBAMYLATION 20
2.4 MULTIPLEXED APPROACHES TO PROTEOMICS 22
2.5 PREFRACTIONATION TOOLS 24
2.5.1 FRACTIONAL CENTRIFUGATION 24
2.5.2 CHROMATOGRAPHIC TECHNIQUES 25
2.5.2.1 GENERAL CHROMATOGRAPHIC METHODS 25
2.5.2.2 SAMPLE FRACTIONATION WITH STACKED SORBENTS 26
2.5.3 ELECTROPHORESIS-BASED METHODS 26
2.5.3.1 CONTINUOUS ELECTROPHORESIS IN FREE LIQUID FILMS 27
2.5.3.2 ROTATIONALLY STABILISED FOCUSING APPARATUS:
THE ROTOFOR 28
2.5.3.3 SAMPLE PREFRACTIONATION VIA MULTICOMPARTMENT
ELECTROLYSERS WITH ISOELECTRIC MEMBRANES 28
2.5.3.4 MINIATURISED ISOELECTRIC SEPARATION DEVICES 30
2.6 OTHER METHODS FOR PREFRACTIONATION OF SAMPLES 30
XVIII CONTENTS
2.6.1 DEPLETIO
N O
F HIGH-ABUNDANC
E PROTEIN
S .
. 3
0
2.6.2 EQUALISE
R BEADS
: TH
E DEMOCRATI
C VERSU
S
TH
E PLUTOCRATI
C PROTEOM
E .
. 3.1
2.7 CONCLUSION
S 35
REFERENCES .3
6
3 PROTEI
N IDENTIFICATIO
N I
N PROTEOMIC
S .
. 4
1
PATRICIA HERNANDEZ, PIERRE-ALAIN BINZ, AND MAR
C
R.
WILKINS
3.1 INTRODUCTIO
N 41
3.2 ATTRIBUTE
S OF PROTEIN
S USEFUL FOR THEI
R IDENTIFICATIO
N . 42
3.2.1 SPECIE
S OF ORIGI
N 42
3.2.2 PROTEI
N ISOELECTRI
C POIN
T 4
2
3.2.3 PROTEI
N MASS 42
3.2.4 PARTIA
L SEQUENC
E O
R SEQUENC
E TA
G 4
3
3.2.5 PROTEI
N AMIN
O ACI
D COMPOSITIO
N 4
3
3.3 PROTEI
N IDENTIFICATIO
N B
Y MAS
S SPECTROMETR
Y 4
5
3.3.1 'TOP-DOWN
' VERSU
S 'BOTTOM-UP
' STRATEGIE
S FOR PROTEI
N
IDENTIFICATIO
N 4
5
3.3.2 INTRODUCTIO
N T
O MAS
S SPECTROMETR
Y 4
7
3.3.2.1 IONISATIO
N 47
3.3.2.2 MASS ANALYSI
S 48
3.3.2.3 INSTRUMENTATIO
N 5
0
3.3.3 PROTEI
N IDENTIFICATIO
N B
Y PEPTID
E MAS
S FINGERPRINTIN
G 5
1
3.3.3.1 PRINCIPL
E 51
3.3.3.2 IDENTIFICATIO
N AN
D CHARACTERISATIO
N O
F MODIFIE
D
PEPTIDE
S B
Y PEPTID
E MAS
S FINGERPRINTIN
G 5
3
3.3.3.3 LIMITATION
S O
F PEPTID
E MAS
S FINGERPRINTIN
G 5
5
3.3.4 TANDE
M MASS SPECTROMETR
Y BASE
D IDENTIFICATIO
N 5
6
3.3.4.1 TANDE
M MAS
S SPECTROMETR
Y SPECTR
A 5
6
3.3.4.2 THE 'PEPTID
E FRAGMEN
T FINGERPRINTING
' APPROAC
H 5
7
3.3.4.3 DE NOV
O SEQUENCIN
G 60
3.3.4.4 IDENTIFICATIO
N AN
D CHARACTERISATIO
N O
F PEPTIDE
S
WIT
H UNEXPECTE
D MODIFICATION
S 6
1
3.3.4.5 SPECTRA
L LIBRAR
Y SEARCHE
S 62
3.4 LIST OF TOOL
S AN
D URLS 65
3.5 CONCLUDIN
G REMARK
S 65
REFERENCES 66
4 QUANTITATIO
N IN PROTEOMIC
S 69
GARRY
L.
CORTHALS AND KEITH ROSE
4.1 INTRODUCTION 69
4.2 NON-MASS-SPECTROMETRIC APPROACHES TO QUANTITATION 70
4.3 RELATIVE QUANTITATION BY MASS SPECTROMETRY 74
4.3.1 ABSOLUTE OR RELATIVE QUANTITATION? 76
4.3.2 INTRODUCTION OF STABLE ISOTOPES USING CHEMICAL TAGS 76
4.3.3 ENZYME-MEDIATED INCORPORATION OF STABLE ISOTOPES 80
4.3.4 BIOLOGICAL INCORPORATION OF STABLE ISOTOPES
BY METABOLIC LABELLING 81
CONTENTS XIX
4.3.
5 RELATIV
E QUANTISATIO
N WITHOU
T US
E O
F STABL
E
ISOTOP
E LABELLIN
G .
. 8
2
4.3.
6 ABSOLUT
E QUANTITATIO
N B
Y MAS
S SPECTROMETR
Y .
. 8
2
4.
4 ANALYSI
S O
F KNOW
N POST-TRANSLATIONA
L MODIFICATION
S .
. 8
3
4.4.
1 GLYCOSYLATION.
. 8
3
4.4.2
PHOSPHORYLATION 85
4.4.3
UBIQUITINYLATION 87
4.5 CONCLUSIONS 87
REFERENCES 88
5 ONE GENE, MANY PROTEIN
S 95
NICOLLE
H.
PACKER, ANDREW
A.
GOOLEY, AND MARC
R.
WILKINS
5.1 INTRODUCTION 95
5.2 AN OVERVIEW OF MODIFICATIONS: WHAT ARE THEY AN
D WHERE
DO THEY OCCUR? 99
5.3 HOW DO WE FIND POST-TRANSLATIONAL MODIFICATIONS? 100
5.3.1 SEPARATION OF ISOFORMS 100
5.3.2 DETECTION OF CO- AND POST-TRANSLATIONAL MODIFICATIONS 102
5.3.3 STRATEGY FOR THE ANALYSIS OF MODIFICATIONS:
TOP DOWN VERSUS BOTTOM UP 103
5.3.4 MASS SPECTROMETRY FOR ANALYSIS OF CO- AN
D
POST-TRANSLATIONAL MODIFICATIONS 104
5.4 ANALYSIS OF SPECIFIC MODIFICATIONS 105
5.4.1 ACETYLATION 106
5.4.2 PHOSPHORYLATION 106
5.4.3 UBIQUITINATION AND SUMOYLATION 107
5.4.4 GLYCOSYLATION 107
5.5 THE FUNCTION OF PROTEIN POST-TRANSLATIONAL MODIFICATIONS:
MORE THAN MEETS THE EYE? 109
5.6 SOME INTERESTING MODIFICATION STORIES IL
L
5.6.1 THE ERYTHROPOIETIN STORY IL
L
5.6.2 THE APOLIPOPROTEIN E STORY 113
5.6.3 THE PROGERIA STORY 114
5.6.4 THE INFLUENZA STORY 115
5.7 FUTURE DIRECTIONS 116
REFERENCES 116
6 PROTEOME IMAGING 123
PATRICIA
M.
PALAGI, DANIEL WALTHER, CATHERINE
G.
ZIMMERMANN-IVOL,
AND RON
D.
APPEL
6.1 INTRODUCTION 123
6.2 IMAGE ANALYSIS OF TWO-DIMENSIONAL ELECTROPHORESIS GELS 124
6.2.1 FIRST STEPS IN GEL IMAGE ANALYSIS 125
6.2.2 APPLICATIONS TO DIFFERENT PROTEOMICS APPROACHES 127
6.2.2.1 SINGLE-GEL ANALYSIS 128
6.2.2.2 GROUPS OF GELS 128
6.2.2.3 TWO-DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS 128
XX CONTENTS
6.
3 LIQUI
D CHROMATOGRAPHY-MAS
S SPECTROMETR
Y .
. 130
6.3.1 FIRS
T STEP
S I
N LIQUI
D CHROMATOGRAPHY-MAS
S
SPECTROMETR
Y IMAG
E ANALYSI
S .
. 130
6.3.2 APPLICATION
S T
O DIFFEREN
T PROTEOMIC
S APPROACHE
S .13
1
6.3.2.
1 MONITORIN
G EXPERIMENT
S AN
D POST-TRANSLATIONA
L
MODIFICATION
S .
. 131
6.3.2.
2 SAMPL
E POPULATION
S .
. 132
6.
4 TH
E MOLECULA
R SCANNE
R .
. 134
6.
5 IMAGIN
G MAS
S SPECTROMETR
Y .
. 138
6.5.1 IMAGIN
G MAS
S SPECTROMETR
Y - TECHNICA
L ASPECT
S 13
9
6.5.2 IMAGIN
G MAS
S SPECTROMETR
Y - APPLICATION
S 140
6.
6 CONCLUSIO
N 141
REFERENCE
S 142
7 DAT
A INTEGRATIO
N I
N PROTEOMIC
S 145
FREDERIQUE LISACEK, CHRISTINE HOOGLAND, LYDIE BOUGUELERET, AND AMOS
BAIROCH
7.1 INTRODUCTION 145
7.2 INTEGRATION AS GATHERING AND CROSS-LINKING INFORMATION 148
7.2.1 SELECTION OF SOURCES AN
D QUANTIFICATION 148
7.2.1.1 TRENDS IN DATABASES 148
7.2.1.2 DATA EVOLUTION 149
7.2.2 BIOLOGY INSPIRED CROSS-LINKING 150
7.2.2.1 THE UNIPROT UNIVERSAL PROTEIN KNOWLEDGEBASE 150
7.2.2.2 HUMAN PROTEI
N ATLAS 152
7.2.3 INTEGRATING ELEMENTS OF THE PROTEOMICS WORKFLOW 153
7.2.3.1 HIGH-THROUGHPUT DATA: STANDARDS AND REPOSITORIES .
. 153
7.2.3.2 SWISS-2DPAGE 154
7.2.3.3 PEPTIDEATLAS AN
D THE GLOBAL PROTEOME MACHINE 155
7.2.3.4 OTHER NOTEWORTHY EFFORTS 156
7.2.4 INTEGRATION AS A FEDERATED EFFORT 156
7.2A.I
PROTEOMICS SERVERS 156
7.2.4.2 SEMANTIC WEB APPROACH 158
7.3 INTEGRATION AS BLENDING OF INFORMATION 159
7.3.1 TEXTUAL INFORMATION 159
7.3.2 ONTOLOGIES 160
7.3.3 EXAMPLES OF VISUALISATION TOOLS MERGING SEVERAL SOURCES 161
7.3.4 FROM DATA INTEGRATION TO SYSTEMS BIOLOGY 162
7.4 CONCLUDING REMARKS 164
REFERENCES 164
8 PROTEIN-PROTEIN INTERACTIONS 169
ANNE-CLAUDE GAVIN
8.1 INTRODUCTION 169
8.2 PROTEIN-PROTEI
N INTERACTIONS IN HUMAN DISEASES: ALTERED PROTEIN
CONNECTIVITY LEADS TO DISORDER 170
8.3 CHARTING PROTEIN-PROTEI
N INTERACTIONS 172
8.3.1 CHARACTERISATION OF ALL CODING SEQUENCES
IN AN ORGANISM 175
CONTENT
S XXI.
8.3.
2 MONITORIN
G BINAR
Y INTERACTIONS
: TH
E YEAS
T
TWO-HYBRI
D SYSTE
M 17
5
8.3.
3 ANALYSI
S O
F PROTEI
N COMPLEXE
S B
Y AFFINIT
Y PURIFICATIO
N
AN
D MAS
S SPECTROMETR
Y .
. 17
7
8.3.
4 LUMINESCENCE-BASE
D MAMMALIA
N INTERACTOM
E MAPPIN
G .
. 18
0
8.3.
5 PROTEI
N MICROARRAY
S 18
0
8.3.
6 DAT
A QUALIT
Y 18
0
8.4 BIOLOGICA
L AN
D BIOMEDICA
L APPLICATION
S . 18
1
8.4.
1 CHARTIN
G O
F
DISEASE
S AN
D
PHARMACOLOGICALL
Y
RELEVAN
T
PATHWAY
S
18
1
8.4.
2
LESSON
S LEARNE
D FRO
M GLOBA
L
INTERACTIO
N ANALYSE
S I
N YEAS
T .
. 18
2
8.4.
3
A
N
EMERGIN
G APPLICATION
: TH
E DEVELOPMEN
T
O
F SMALL-MOLECUL
E PROTEIN-PROTEI
N INTERACTIO
N INHIBITOR
S .
. 18
4
8.5 FUTUR
E DIRECTION
S 186
REFERENCE
S 18
7
9 BIOMEDICA
L APPLICATION
S O
F PROTEOMIC
S 19
3
JEAN-CHARLES SANCHEZ,
YOHANN
COUTE,
LAURE
ALLARD,
PIERRE LESCUYER, AND DENI
S
F.
HOCHSTRASSER
9.1 INTRODUCTIO
N 193
9.2 THE APPLICATION OF PROTEOMIC
S TO MEDICIN
E 194
9.3 DISEAS
E DIAGNOSIS FROM BODY FLUIDS 196
9.4 VASCULAR DISEASES 197
9.4.1 INTRODUCTION 197
9.4.2 APPLICATION OF PROTEOMICS TO VASCULAR DISEASE
S
AND ATHEROSCLEROSIS 198
9.4.3 APPLICATION OF PROTEOMICS TO CARDIOVASCULAR DISEASE
S 199
9.4.4 APPLICATION OF PROTEOMICS TO CEREBROVASCULAR DISEASE 200
9.4.5 CONCLUSION 201
9.5 NEURODEGENERATIVE DISORDERS 202
9.5.1 BRAIN PROTEOM
E 202
9.5.2 PROTEOMIC PROFILING OF NEURODEGENERATIV
E DISORDER
S 203
9.5.3 CEREBROSPINAL FLUID PROTEIN MARKERS 205
9.6 PROTEOMIC
S AND CANCER 206
9.6.1 BIOMARKER DISCOVER
Y IN CANCER PROTEOMIC
S 207
9.6.1.1 TISSUE
S 207
9.6.1.2 PRIMARY AND ESTABLISHED CELL LINES 208
9.6.2 PROTEOMIC PROFILING IN ONCOLOG
Y 209
9.6.2.1 SURFACE-ENHANCED LASER DESORPTION/IONISATIO
N
TIME-OF-FLIGHT MASS SPECTROMETRY .21
0
9.6.2.2 PROTEIN MICROARRAYS 210
9.6.2.3 TISSU
E PROFILING BY MATRIX-ASSISTED LASER
DESOPRTIOON/IONISATIO
N MASS SPECTROMETRY IMAGING .
. 210
9.6.3 USE OF PROTEOMIC
S TO DEFINE THE TISSUE OF ORIGIN 211
9.6.4 CONCLUSION 211
9.7 TOXICOPHARMACOLOGY
: THE EXAMPLE OF TYPE 2 DIABETE
S 211
9.7.1 INTRODUCTION TO DIABETES 212
9.7.2 PATHOGENESIS OF TYPE 2 DIABETE
S 212
XXII CONTENTS
9.7.3 TREATMENT
S O
F TYP
E 2 DIABETE
S .
. 21
3
9.7.4 PROTEOMIC
S FOR TH
E DISCOVER
Y O
F TREATMEN
T TARGET
S
FOR TYPE 2 DIABETE
S .
. 21
3
9.8 CURREN
T LIMITATION
S AN
D FUTUR
E DIRECTION
S O
F PROTEOMIC
S
FOR MEDICIN
E 215
9.8.1 PREANALYTICA
I ISSUE
S .21
5
9.8.2 ANALYTICA
L ASPECT
S 216
9.8.3 POSTANALYTICA
L ASPECT
S 21
7
9.9 PRESEN
T AN
D FUTUR
E DIRECTION
S 217
REFERENCE
S 21
7
10 PROTEOMICS
: WHERE TO NEXT?
.
22
3
KEITH
L.
WILLIAMS AND DENIS
F.
HOCHSTRASSER
10.1 INTRODUCTIO
N 223
10.2 THE RELEVANCE OF -OMIC
S TO BIOLOGY 22
4
10.3 TECHNOLOGICA
L DEVELOPMENT
S IN PROTEOMIC
S 22
5
10.3.1 CHARACTERISING MODIFICATIONS 226
10.3.2 GLOBAL TISSUE ANALYSI
S 226
10.4 THE NEX
T STEPS FOR PROTEOMICS
: DIAGNOSTIC
S AN
D DRUGS 22
7
10.4.1 DIAGNOSTIC
S 228
10.4.2 DRUG
S 228
10.5 CONCLUSION
S 229
REFERENCES 229
INDE
X 231
PPN: 265755956
TITEL: PROTEOME RESEARCH : CONCEPTS, TECHNOLOGY AND APPLICATION / M. R.
WILKINS . (EDS.). - . -
BERLIN : SPRINGER, 2007
ISBN: 978-3-540-71240-4GB.EUR 149.75 (FREIER PR.), SFR 229.50 (FREIER
PR.); 3-540-71240
2GB.EUR 149.75 (FREIER PR.), SFR 229.50 (FREIER PR.)
BIBLIOGRAPHISCHER DATENSATZ IM SWB-VERBUND |
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| dewey-full | 572.6 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
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| discipline | Biologie |
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| spelling | Proteome research concepts, technology and application ; with 16 tables M. R. Wilkins ... (eds.) 2. ed. Berlin [u.a.] Springer 2007 1 Online-Ressource txt rdacontent c rdamedia cr rdacarrier Principles and practice Proteom (DE-588)4576155-3 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Proteom (DE-588)4576155-3 s DE-604 Wilkins, Marc R. Sonstige oth https://doi.org/10.1007/978-3-540-72910-5 Verlag Volltext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016224586&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Proteome research concepts, technology and application ; with 16 tables Proteom (DE-588)4576155-3 gnd |
| subject_GND | (DE-588)4576155-3 (DE-588)4143413-4 |
| title | Proteome research concepts, technology and application ; with 16 tables |
| title_auth | Proteome research concepts, technology and application ; with 16 tables |
| title_exact_search | Proteome research concepts, technology and application ; with 16 tables |
| title_exact_search_txtP | Proteome research concepts, technology and application ; with 16 tables |
| title_full | Proteome research concepts, technology and application ; with 16 tables M. R. Wilkins ... (eds.) |
| title_fullStr | Proteome research concepts, technology and application ; with 16 tables M. R. Wilkins ... (eds.) |
| title_full_unstemmed | Proteome research concepts, technology and application ; with 16 tables M. R. Wilkins ... (eds.) |
| title_short | Proteome research |
| title_sort | proteome research concepts technology and application with 16 tables |
| title_sub | concepts, technology and application ; with 16 tables |
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