Principles of proteomics:
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| Main Author: | |
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| Format: | Book |
| Language: | English |
| Published: |
New York, NY [u.a.]
Garland Science
2014
|
| Edition: | 2. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XI, 260 S., [4] Bl. Ill., graph. Darst. |
| ISBN: | 9780815344728 |
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| 100 | 1 | |a Twyman, Richard M. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Principles of proteomics |c Richard M. Twyman |
| 250 | |a 2. ed. | ||
| 264 | 1 | |a New York, NY [u.a.] |b Garland Science |c 2014 | |
| 300 | |a XI, 260 S., [4] Bl. |b Ill., graph. Darst. | ||
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| adam_text | VIII
Contents
Chapter
1
The origin and scope
of proteomics
1
1.1
INTRODUCTION
1
1.2
THE BIRTH OF LARGE-SCALE BIOLOGY
ANDTHE-OMICS-ERA
1
1.3
THE GENOME,
TRANSCRIPTOME,
PROTEOME, AND METABOLOME
6
1.4
FUNCTIONAL GENOMICS
8
Transcriptomics is the systematic, global
analysis of
m
RNA
8
Large-scale mutagenesis and interference can
also determine the functions of genes on a
global scale
11
1.5
THE NEED FOR PROTEOMICS
15
1.6
THE SCOPE OF PROTEOMICS
17
Protein identification and quantitation are
the most fundamental aspects of proteomic
analysis
17
Important functional data can be gained from
sequence and structural analysis
18
Interaction proteomics and activity-based
proteomics can help to link proteins into
functional networks
19
1.7
CURRENT CHALLENGES IN PROTEOMICS
20
Chapter
2
Strategies for
protein separation
23
2.1
INTRODUCTION
23
2.2
GENERAL PRINCIPLES OF PROTEIN
SEPARATION IN PROTEOMICS
23
2.3
PRINCIPLES OF TWO-DIMENSIONAL GEL
ELECTROPHORESIS
25
Electrophoresis separates proteins by mass
and charge
25
Isoelectric focusing separates proteins by
charge irrespective of mass
26
SDS-PAGE separates proteins by mass
irrespective of charge
28
2.4
THE APPLICATION OF 2DGE IN
PROTEOMICS
29
The four major advantages of 2DGE are
robustness, reproducibility, visualization, and
compatibility with downstream microanalysis
29
The four major limitations of 2DGE are
resolution, sensitivity, representation, and
compatibility with automated protein analysis
30
The resolution of 2DGE can be improved with
giant gels, zoom gels, and modified gradients,
or by pre-ffactiofiating the sample
30
.
The sensitivity of 2DGE depends on the visualization
of minor protein sppts, which
ľ
can be masked by abundant proteins
31
Ttiè
repłe&ntatioiri
of hydrophobic proteins is
ľi
-.-.
an intractable
probte
m
reflecting the
buffelt o«« t
required for isoelectric focusing
32
Downstream mass spectrometry requires Spot
analysis and picking
34
2.5
PRINCIPLES OF MULTIDIMENSIONAL
UQUID CHROMATOGRAPHY
34
Protein and
peptide
separation by
chromatography relies on differing affinity
for stationary and mobile phases
34
Affinity chromatography exploits the specific
binding characteristics of proteins and/or
peptides
36
Size exclusion chromatography sieves
molecules on the basis of their size
36
Ion exchange chromatography exploits
differences in net charge
37
Reversed-phase chromatography and
hydrophobic interaction chromatography
exploit the affinity between peptides and
hydrophobic resins
38
2.6
MULTIDIMENSIONAL UQUID
CHROMATOGRAPHY STRATEGIES IN
PROTEOMICS
39
Multidimensional liquid chromatography is
more versatile and more easily automated than
2DGE but lacks a visual dimension
39
The most useful MDLC systems achieve
optimal peak capacity by exploiting orthogonal
separations that have internally compatible
buffers
40
MudPIT shows how MDLC has evolved from a
laborious technique to virtually hands-free
operation
41
RP-RPLC and HILIC-RP systems offer advantages
for the separation of certain types of
peptide
mixtures
44
Affinity chromatography is combined with MDLC
to achieve the simplification of
peptide
mixtures
44
CONTENTS ¡x
Chapter
3
Strategies for
protein identification
3.1
INTRODUCTION
3.2
PROTEIN IDENTIFICATION WITH
ANTIBODIES
3.3
DETERMINATION OF PROTEIN
SEQUENCES BY CHEMICAL
DEGRADATION
Complete hydrolysis allows protein sequences
to be inferred from the content of the resulting
amino
acid pool
Edman
degradation was the first general
method for the
de novo
sequencing of
proteins
Edman
degradation was the first protein
identification method to be applied in
.
prateomics, but it is difficult to apply on a
large scale
3.4
MASS SPECTROMETRY—BASIC
PRINCIPLES AND INSTRUMENTATION
Mass spectrometry is based on the separation
of molecules according to their mass/charge
ratio
The integration of mass spectrometry into
proteomics required the development of
soft ionization methods to prevent random
fragmentation
Controlled fragmentation is used to break
peptide
bonds and generate fragment ions
Five principal types of mass analyzer are
commonly used in proteomics
3.5
PROTEIN IDENTIFICATION USING DATA
FROM MASS SPECTRA
Peptide
mass fingerprinting correlates
e
xperimental and theoretical intact
peptide
masses
Shotgun proteomics can be combined with
database searches based on uninterpreted
spectra
MS/MS spectra can be used to derive protein
sequences
de novo
Chapter
4
Strategies for
protein quantitation
4.1
INTRODUCTION
4.2
QUANTITATIVE PROTEOMICS BASED
ON 2DGE
The quantitation of proteins in two-dimensional
gels involves the creation of digital data from
analog images
Spot detection, quantitation, and comparison
can be challenging without human intervention
47
47
47
48
48
49
50
52
52
52
53
54
58
58
61
61
69
69
70
70
71
4.3
MULTIPLEXED IN-GEL PROTEOMICS
75
Difference in-gel electrophoresis involves the
simultaneous separation of comparative
protein samples labeled with different
fluorophores
75
Parallel analysis with multiple dyes can
also be used to identify particular structural
or functional groups of proteins
76
4.4
QUANTITATIVE MASS SPECTROMETRY
77
Label-free quantitation may be based on
spectral counting or the comparison of signal
intensities across samples in a narrow m/z
range
77
Label-based quantitation involves the
incorporation of labels that allow
corresponding peptides in different
samples to be identified by a specific change
in mass
77
ICAT reagents are used for the selective
labeling of proteins or peptides
79
Proteins and peptides can also be labeled
nonselectively
80
Isobaric tagging allows protein quantitation
by the detection of reporter ions
80
Metabolic labeling introduces the label before
sample preparation but is limited to simple
organisms and cultured cells
83
Chapter
5
The analysis of
protein sequences
87
5.1
INTRODUCTION
87
5.2
PROTEIN FAMILIES AND
EVOLUTIONARY RELATIONSHIPS
89
Evolutionary relationships between proteins
are based on homology
89
The function of a protein can often be
predicted from its sequence
92
5.3
PRINCIPLES OF PROTEIN SEQUENCE
COMPARISON
93
Protein sequences can be compared in terms
of identity and similarity
93
Homologous sequences are found by pairwise
similarity searching
93
Substitution score matrices rank the
importance of different substitutions
96
Sequence alignment scores depend on
sequence length
98
Multiple alignments provide more information
about key sequence elements
98
5.4
STRATEGIES TO FIND MORE DISTANT
RELATIONSHIPS
100
PSI-BLAST uses sequence profiles to carry out
iterative searches
ЮО
CONTENTS
5.5
Pattern recognition methods incorporate
conserved sequence signatures
THE RISK OF FALSE-POSITIVE
ANNOTATIONS
Chapter
6
The analysis of
i Structures
101
104
107
6.1
INTRODUCTION
107
6.2
STRUCTURAL GENOMICS AND
STRUCTURE
SPACE
110
Coverage of
structure
space is currently
uneven
110
Structure and function are not always related
113
6.3
TECHNIQUES FOR SOLVING PROTEIN
STRUCTURES
114
X-ray diffraction requires well-ordered protein
crystals
114
NMR spectroscopy exploits the magnetic
properties of certain atomic nuclei
116
Additional methods for structural analysis
mainly provide supporting data
118
6.4
PROTEIN STRUCTURE PREDICTION
119
Structural predictions can bridge the gap
between sequence and structure
119
Protein secondary structures can be
predicted from sequence data
120
Tertiary structures can be predicted by
comparative modeling if a template
structure is available
122
Ab initio
prediction methods attempt to
construct structures from first principles
123
Fold recognition (threading) is based on
similarities between nonhomologous folds
123
6.5
COMPARISON OF PROTEIN
STRUCTURES
124
6.6
STRUCTURAL CLASSIFICATION OF
PROTEINS
125
6.7
GLOBAL STRUCTURAL GENOMICS
INITIATIVES
126
Chápte
7
Interaction
proteomics
131
7.1
INTRODUCTION
131
7.2
METHODS TO STUDY
PROTEIN-PROTEIN INTERACTIONS
134
Genetic methods suggest interactions from
the combined effects of two mutations in
the same cell or organism
134
Protein interactions can be suggested by
comparative genomics and homology transfer
135
Affinity-based biochemical methods provide
direct evidence that proteins can interact
138
Interactions between proteins in vitro and
in vivo can be established by resonance
energy transfer
142
Surface plasmon resonance can indicate the
mass of interacting proteins
142
7.3
LIBRARY-BASED METHODS FOR THE
GLOBAL ANALYSIS OF BINARY
INTERACTIONS
143
7.4
TWO-HYBRID/PROTEIN
COMPLEMENTATION ASSAYS
145
The yeast two-hybrid system works by
assembling a transcription factor from two
inactive fusion proteins
145
Several large-scale interaction screens have
been carried out using different yeast
two-hybrid screening strategies
146
Conventional yeast two-hybrid screens have
a significant error rate
148
7.5
MODIFIED TWO-HYBRID SYSTEMS
FOR MEMBRANE, CYTOSOUC, AND
EXTRACELLULAR PROTEINS
149
7.6
BACTERIAL AND MAMMALIAN
TWO-HYBRID SYSTEMS
150
7.7
LUMIER AND MAPPIT HIGH-
THROUGHPUT TWO-HYBRID
PLATFORMS
151
7.8
ADAPTED HYBRID ASSAYS FOR
DIFFERENT TYPES OF INTERACTIONS
152
7.9
SYSTEMATIC COMPLEX ANALYSIS
BY TANDEM AFFINITY PURIFICATION-
MASS SPECTROMETRY
153
7.10
ANALYSIS OF PROTEIN INTERACTION
DATA
155
7.11
PROTEIN INTERACTION MAPS
156
7.12
PROTEIN INTERACTIONS WITH SMALL
MOLECULES
158
Chapter
8
Protein
modification in proteomics
Protein phosphorylation is a key regulatory
mechanism
165
165
8.1
INTRODUCTION
8.2
METHODS FOR THE DETECTION OF
POST-TRANSLATIONAL MODIFICATIONS
167
8.3
ENRICHMENT STRATEGIES FOR
MODIFIED PROTEINS AND PEPTIDES
168
8.4
PHOSPHOPROTEOMICS
170
170
Separated phosphoproteins can be detected
with specific staining reagents
172
CONTENTS
Xl
Sample
preparation for phosphoprotein
analysis typically involves enrichment
using antibodies or strongly cationic
chromatography resins
173
8.5
ANALYSIS OF PHOSPHOPROTEINS BY
MASS SPECTROMETRY
176
A combination of
Edman
degradation and
mass spectrometry can be used to map
phosphorylation sites
176
Intact phosphopeptide ions can be identified
by MALDI-TOF mass spectrometry
176
Phosphopeptides yield diagnostic marker ions
and neutral loss products
177
8.6
QUANTITATIVE ANALYSIS OF
PHOSPHOPROTEINS
180
8.7
GLYCOPROTEOMICS
181
Glycoproteins represent more than half of
the eukaryotic proteome
181
Glycans play important roles in protein
stability, activity, and localization, and are
important indicators of disease
183
Conventional glycoanalysis involves the use
of enzymes that remove specific glycan
groups and the separation of glycoproteins
by electrophoresis
184
Glycoprotein-specific staining allows the
glycoprotein to be studied by 2DGE
187
There are two principal methods for
glycoprotein enrichment that have
complementary uses
188
Mass spectrometry is used for the high-
throughput identification and
characterization of glycoproteins
189
Chapter
9
Protein microarrays 191
9.1
INTRODUCTION
191
9.2
THE EVOLUTION OF PROTEIN
MICROARRAYS
191
9.3
DIFFERENT TYPES OF PROTEIN
MICROARRAYS
193
Analytical, functional, and reverse microarrays
are distinguished by their purpose and the
nature of the interacting components
193
Analytical microarrays contain antibodies
or other capture reagents
194
Functional protein microarrays can be used
to study a wide range of biochemical
functions
196
9.4
THE MANUFACTURE OF FUNCTIONAL
PROTEIN MICROARRAYS—PROTEIN
SYNTHESIS
197
Proteins can be synthesized by the parallel
construction of many expression vectors
197
Cell-free expression systems allow the direct
synthesis of protein arrays in situ
9.5
THE MANUFACTURE OF FUNCTIONAL
PROTEIN MICROARRAYS—PROTEIN
IMMOBILIZATION
9.6
THE DETECTION OF PROTEINS ON
MICROARRAYS
Methods that require labels can involve
either direct or indirect detection
Label-free methods do not affect the
intrinsic properties of interacting proteins
9.7
197
201
203
203
204
EMERGING PROTEIN CHIP
TECHNOLOGIES
207
Bead and particle arrays in solution represent
the next generation of protein microarrays
207
Cell and tissue arrays allow the direct
analysis of proteins in vivo
207
Chapter
10
Applications
of proteomics
211
10.1
INTRODUCTION
211
10.2
DIAGNOSTIC APPLICATIONS OF
PROTEOMICS
212
Proteomics is used to identify
biomarkers
of
disease states
212
Biomarkers
can be discovered by finding
plus/minus or quantitative differences
between samples
215
More sensitive techniques can be used to
identify
biomarker
profiles
218
10.3
APPLICATIONS OF PROTEOMICS IN
DRUG DEVELOPMENT
219
Proteomics can help to select drug targets
and develop lead compounds
219
Proteomics is also useful for target validation
222
Chemical proteomics can be used to select
and develop lead compounds
222
Proteomics can be used to assess drug
toxicity
during clinical development
224
10.4
PROTEOMICS IN AGRICULTURE
225
Proteomics provides novel markers in plant
breeding and genetics
225
Proteomics can be used for the analysis of
genetically modified plants
227
10.5
PROTEOMICS IN INDUSTRY-
IMPROVING THE YIELD OF
SECONDARY METABOLISM
228
Glossary
231
Index
248
|
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| indexdate | 2024-07-10T00:42:22Z |
| institution | BVB |
| isbn | 9780815344728 |
| language | English |
| lccn | 2013021694 |
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| spelling | Twyman, Richard M. Verfasser aut Principles of proteomics Richard M. Twyman 2. ed. New York, NY [u.a.] Garland Science 2014 XI, 260 S., [4] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Proteomics Proteins Proteom (DE-588)4576155-3 gnd rswk-swf Proteomanalyse (DE-588)4596545-6 gnd rswk-swf Proteom (DE-588)4576155-3 s Proteomanalyse (DE-588)4596545-6 s DE-604 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026193229&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Twyman, Richard M. Principles of proteomics Proteomics Proteins Proteom (DE-588)4576155-3 gnd Proteomanalyse (DE-588)4596545-6 gnd |
| subject_GND | (DE-588)4576155-3 (DE-588)4596545-6 |
| title | Principles of proteomics |
| title_auth | Principles of proteomics |
| title_exact_search | Principles of proteomics |
| title_full | Principles of proteomics Richard M. Twyman |
| title_fullStr | Principles of proteomics Richard M. Twyman |
| title_full_unstemmed | Principles of proteomics Richard M. Twyman |
| title_short | Principles of proteomics |
| title_sort | principles of proteomics |
| topic | Proteomics Proteins Proteom (DE-588)4576155-3 gnd Proteomanalyse (DE-588)4596545-6 gnd |
| topic_facet | Proteomics Proteins Proteom Proteomanalyse |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026193229&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT twymanrichardm principlesofproteomics |