Proteomics in practice: a guide to successful experimental design
Gespeichert in:
| Hauptverfasser: | , , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Weinheim
Wiley-VCH
2008
|
| Ausgabe: | 2., completely rev. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | XX, 482 S. zahlr. Ill., graph. Darst. |
| ISBN: | 9783527319411 3527319417 |
Internformat
MARC
| LEADER | 00000nam a2200000 c 4500 | ||
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| 003 | DE-604 | ||
| 005 | 20140311 | ||
| 007 | t | ||
| 008 | 080409s2008 gw ad|| |||| 00||| eng d | ||
| 015 | |a 07,N47,0991 |2 dnb | ||
| 016 | 7 | |a 986204390 |2 DE-101 | |
| 020 | |a 9783527319411 |c Gb. : ca. EUR 89.00 (freier Pr.), ca. sfr 142.00 (freier Pr.) |9 978-3-527-31941-1 | ||
| 020 | |a 3527319417 |c Gb. : ca. EUR 89.00 (freier Pr.), ca. sfr 142.00 (freier Pr.) |9 3-527-31941-7 | ||
| 024 | 3 | |a 9783527319411 | |
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| 100 | 1 | |a Westermeier, Reiner |d 1951- |e Verfasser |0 (DE-588)135840627 |4 aut | |
| 245 | 1 | 0 | |a Proteomics in practice |b a guide to successful experimental design |c Reiner Westermeier, Tom Naven, and Hans-Rudolf Höpker |
| 250 | |a 2., completely rev. ed. | ||
| 264 | 1 | |a Weinheim |b Wiley-VCH |c 2008 | |
| 300 | |a XX, 482 S. |b zahlr. Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 7 | |a Proteins |2 cabt | |
| 650 | 7 | |a Analytical Methods |2 cabt | |
| 650 | 7 | |a PAGE |2 cabt | |
| 650 | 7 | |a Electrophoresis |2 cabt | |
| 650 | 7 | |a Chromatogrphy |2 cabt | |
| 650 | 7 | |a Spectrometry |2 cabt | |
| 650 | 0 | 7 | |a Proteomanalyse |0 (DE-588)4596545-6 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4127380-1 |a Praktikum |2 gnd-content | |
| 689 | 0 | 0 | |a Proteomanalyse |0 (DE-588)4596545-6 |D s |
| 689 | 0 | |5 DE-604 | |
| 700 | 1 | |a Naven, Tom |e Verfasser |4 aut | |
| 700 | 1 | |a Höpker, Hans-Rudolf |e Verfasser |4 aut | |
| 856 | 4 | 2 | |q text/html |u http://deposit.dnb.de/cgi-bin/dokserv?id=3019253&prov=M&dok_var=1&dok_ext=htm |3 Inhaltstext |
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| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-016432719 | |
Datensatz im Suchindex
| _version_ | 1805090264691245056 |
|---|---|
| adam_text |
Contents
Preface
XI
Foreword
XIII
Abbreviations, Symbols, Units XV
Introduction
1
1
History
1
2
Critical Points
8
2.1
Challenges of the Protein Samples
8
2.1
Challenges of the Analysis Systems
11
3
Proteomics Strategies
12
3.1
Proteome Mapping
12
3.2
Differential Analysis
12
3.3
Time Point Experiments
13
3.4
Verification of Targets or
Biomarkers
13
3.5
Integration of Results into Biological Context
13
3.6
Systems Biology
13
4
Concept of Experimental Planning
14
4.1
Biological Replicates
14
4.2
Pooling of Samples: Yes or No?
14
4.3
Pre-fractionation of Samples: Yes or No?
14
4.4
Which is the Best Workflow to Start With?
35
Part I: Proteomics Technology
1
Electrophoretic Techniques
19
1.1
The Principle of Electrophoresis and Some Methodological
Background
19
1.1.1
Free Flow Electrophoretic Methods
20
1.1.2
Gels for Electrophoretic Techniques
21
1.1.3
Electroendosmosis Effects
21
1.2
Polyacrylamide Gel Electrophoresis
22
VI
I Contents
1.2.1
The Polyacrylamide Gel
22
1.2.2
SDS
Polyacrylamide Gel Electrophoresis
27
1.2.3
Blue Native Electrophoresis
32
1.2.4
Cationic Detergent Electrophoresis
34
1.3
Blotting
35
1.3.1
Electrophoretic Transfer
36
1.3.2
Protein Detection on the Membrane
36
1.4
Isoelectric Focusing
38
1.4.1
Theoretical Background
39
1.4.2
Preparation of IEF Gels
44
1.4.3
Isoelectric Focusing in Proteomics
45
1.5
Two-dimensional Electrophoresis
53
1.5.1
Sample Preparation
53
1.5.2
Pre-labeling of Proteins for Difference Gel Electrophoresis
68
1.5.3
First Dimension: Isoelectric Focusing in IPG Strips
77
1.5.4
Second Dimension:
SDS
Electrophoresis
100
1.5.5
Detection of Protein Spots
229
1.6
Image Analysis
225
1.6.1
Image Acquisition
225
1.6.2
Image Analysis and Evaluation
129
1.6.3
Use ofl-D Electrophoresis Data
137
1.7
Spot Handling
237
1.7.1
Spot Picking
239
1.7.2
Protein Cleavage
242
2
Liquid Chromatography Techniques
252
2.1
Basic Principles of Important Liquid Chromatography
Techniques
252
2.1.1
Ion Exchange Chromatography
253
2.1.2
Reversed Phase Chromatography
262
2.1.3
Affinity Chromatography
267
2.1.4
Gel Filtration
272
2.2
Strategic Approach and General Applicability
274
2.3
Liquid Chromatography Techniques and Applications in Proteome
Analysis
276
2.3.1
Peptide
Separation
276
2.3.2
2DLC
Peptide
Separation
279
2.3.3
Affinity Chromatography and LC-MS/MS
287
2.3.4
Protein Pre-fractionation
289
2.4
Practical Considerations and Application of LC-based Protein
Pre-fractionation
394
2.4.1
Sample Extraction and Preparation
296
2.4.2
Experimental Setup
297
2.4.3
Ion Exchange Chromatography and
Protein Pre-fractionation
298
Contents
VII
2.4.4
Reversed Phase Chromatography and
Protein Pre-fractionation
205
2.4.5
Fraction Size and Number of Fractions
210
2.5
Critical Review and Outlook
211
3
Mass Spectrometry
225
3.1
Ionization
228
3.1.1
Matrix Assisted Laser Desorption Ionization
228
3.1.2
Electrospray Ionization
222
3.2
Ion Separation
225
3.2.1
Time-of-Flight Analyzer
225
3.2.2
Triple Quadrapole Analyzer
227
3.2.3
Quadrapole Ion Trap
228
3.2.4
Quadrupole Time-of-Flight
230
3.2.5
Hybrid Triple Quadrupole Linear Ion Trap
231
3.2.6
TOF/TOF Analyzer
232
3.2.7
Fourier Transform Ion Cyclotron
232
3.2.8
Orbitrap
233
3.3
Generating MS Data for Protein Identification
233
3.3.1
Peptide
Mass Fingerprint
234
3.3.2
Peptide
Mass Fingerprint Combined With Composition
Information
237
3.3.3
Peptide
Mass Fingerprint Combined With Partial Sequence
Information
238
3.3.4
Tandem Mass Spectrometry
242
3.4
Protein Characterization
258
3.4.1
Phosphorylation Analysis
259
3.4.2
Affinity Chromatography
260
3.4.3
Chemical Derivatization
262
3.4.4
Glycosylation
263
3.5
Protein Quantification Using Mass Spectrometry
264
3.5.1
Stable Isotope Labeling Approaches
264
3.5.2
Isotope-coded Affinity Tags
265
3.5.3
Stable Isotope Labeling with
Amino
Acids in Cell Culture
266
3.5.4
AQUA
267
3.5.5
iTRAQ
267
3.5.6
Non-labeling Software Approaches
268
3.6
MS Strategies
272
3.6.1
Bottom up Approach
272
3.6.2
Top down Approach
272
4
Functional Proteomics: Studies of Protein-Protein Interactions
273
4.1
Non-immunological Methods
273
АЛЛ
Separation of Intact Multi-protein Complexes
273
4.1.2
Probing with Interaction Partners
273
Vili
Contents
4.1.3
Surface Plasmon
Resonance
274
4.2
Antibody-based
Techniques
275
A.I.I Western Blotting and Dot Blots
275
4.2.2
Protein Microarrays
276
Part II: Practical Manual of Proteome Analysis
279
Equipment, Consumables, Reagents
281
Step
1:
Sample Preparation
287
Step
2:
Fluorescence Difference Gel Electrophoresis
299
Step
3:
Isoelectric Focusing
309
Step
4:
SDS Polyacrylamide
Gel Electrophoresis
323
Step
5:
Scanning of Gels Containing Pre-labeled Proteins
357
Step
6:
Staining of Gels
361
Step
7:
Image Analysis and Evaluation of DIGE Gels
373
Step
8:
Spot Excision
383
Step
9:
Sample Destaining
387
Step
10:
Protein Digestion
389
Step
11:
Microscale Desalting and Concentrating of Sample
393
Step
12:
Chemical Derivatization of the
Peptide
Digest
397
Step
13:
MS Analysis
399
Step
14:
Calibration of MALDI-ToF MS
403
Step
15:
Preparing for a Database Search
407
Partili:
Troubleshooting
411
1
Two-dimensional Electrophoresis
413
1.1
Sample Preparation
413
1.2
Isoelectric focusing in IGPG strips
414
1.3
SDS
PAGE
416
1.4
Staining
417
Contents
I IX
1.5 DIGE
Fluorescence Labeling
418
1.6
Results in 2-D Electrophoresis
421
2
Mass Spectrometry
429
References
433
Glossary of Terms
462
Index
473
Legal Statements
481 |
| adam_txt |
Contents
Preface
XI
Foreword
XIII
Abbreviations, Symbols, Units XV
Introduction
1
1
History
1
2
Critical Points
8
2.1
Challenges of the Protein Samples
8
2.1
Challenges of the Analysis Systems
11
3
Proteomics Strategies
12
3.1
Proteome Mapping
12
3.2
Differential Analysis
12
3.3
Time Point Experiments
13
3.4
Verification of Targets or
Biomarkers
13
3.5
Integration of Results into Biological Context
13
3.6
Systems Biology
13
4
Concept of Experimental Planning
14
4.1
Biological Replicates
14
4.2
Pooling of Samples: Yes or No?
14
4.3
Pre-fractionation of Samples: Yes or No?
14
4.4
Which is the Best Workflow to Start With?
35
Part I: Proteomics Technology
1
Electrophoretic Techniques
19
1.1
The Principle of Electrophoresis and Some Methodological
Background
19
1.1.1
Free Flow Electrophoretic Methods
20
1.1.2
Gels for Electrophoretic Techniques
21
1.1.3
Electroendosmosis Effects
21
1.2
Polyacrylamide Gel Electrophoresis
22
VI
I Contents
1.2.1
The Polyacrylamide Gel
22
1.2.2
SDS
Polyacrylamide Gel Electrophoresis
27
1.2.3
Blue Native Electrophoresis
32
1.2.4
Cationic Detergent Electrophoresis
34
1.3
Blotting
35
1.3.1
Electrophoretic Transfer
36
1.3.2
Protein Detection on the Membrane
36
1.4
Isoelectric Focusing
38
1.4.1
Theoretical Background
39
1.4.2
Preparation of IEF Gels
44
1.4.3
Isoelectric Focusing in Proteomics
45
1.5
Two-dimensional Electrophoresis
53
1.5.1
Sample Preparation
53
1.5.2
Pre-labeling of Proteins for Difference Gel Electrophoresis
68
1.5.3
First Dimension: Isoelectric Focusing in IPG Strips
77
1.5.4
Second Dimension:
SDS
Electrophoresis
100
1.5.5
Detection of Protein Spots
229
1.6
Image Analysis
225
1.6.1
Image Acquisition
225
1.6.2
Image Analysis and Evaluation
129
1.6.3
Use ofl-D Electrophoresis Data
137
1.7
Spot Handling
237
1.7.1
Spot Picking
239
1.7.2
Protein Cleavage
242
2
Liquid Chromatography Techniques
252
2.1
Basic Principles of Important Liquid Chromatography
Techniques
252
2.1.1
Ion Exchange Chromatography
253
2.1.2
Reversed Phase Chromatography
262
2.1.3
Affinity Chromatography
267
2.1.4
Gel Filtration
272
2.2
Strategic Approach and General Applicability
274
2.3
Liquid Chromatography Techniques and Applications in Proteome
Analysis
276
2.3.1
Peptide
Separation
276
2.3.2
2DLC
Peptide
Separation
279
2.3.3
Affinity Chromatography and LC-MS/MS
287
2.3.4
Protein Pre-fractionation
289
2.4
Practical Considerations and Application of LC-based Protein
Pre-fractionation
394
2.4.1
Sample Extraction and Preparation
296
2.4.2
Experimental Setup
297
2.4.3
Ion Exchange Chromatography and
Protein Pre-fractionation
298
Contents
VII
2.4.4
Reversed Phase Chromatography and
Protein Pre-fractionation
205
2.4.5
Fraction Size and Number of Fractions
210
2.5
Critical Review and Outlook
211
3
Mass Spectrometry
225
3.1
Ionization
228
3.1.1
Matrix Assisted Laser Desorption Ionization
228
3.1.2
Electrospray Ionization
222
3.2
Ion Separation
225
3.2.1
Time-of-Flight Analyzer
225
3.2.2
Triple Quadrapole Analyzer
227
3.2.3
Quadrapole Ion Trap
228
3.2.4
Quadrupole Time-of-Flight
230
3.2.5
Hybrid Triple Quadrupole Linear Ion Trap
231
3.2.6
TOF/TOF Analyzer
232
3.2.7
Fourier Transform Ion Cyclotron
232
3.2.8
Orbitrap
233
3.3
Generating MS Data for Protein Identification
233
3.3.1
Peptide
Mass Fingerprint
234
3.3.2
Peptide
Mass Fingerprint Combined With Composition
Information
237
3.3.3
Peptide
Mass Fingerprint Combined With Partial Sequence
Information
238
3.3.4
Tandem Mass Spectrometry
242
3.4
Protein Characterization
258
3.4.1
Phosphorylation Analysis
259
3.4.2
Affinity Chromatography
260
3.4.3
Chemical Derivatization
262
3.4.4
Glycosylation
263
3.5
Protein Quantification Using Mass Spectrometry
264
3.5.1
Stable Isotope Labeling Approaches
264
3.5.2
Isotope-coded Affinity Tags
265
3.5.3
Stable Isotope Labeling with
Amino
Acids in Cell Culture
266
3.5.4
AQUA
267
3.5.5
iTRAQ
267
3.5.6
Non-labeling Software Approaches
268
3.6
MS Strategies
272
3.6.1
Bottom up Approach
272
3.6.2
Top down Approach
272
4
Functional Proteomics: Studies of Protein-Protein Interactions
273
4.1
Non-immunological Methods
273
АЛЛ
Separation of Intact Multi-protein Complexes
273
4.1.2
Probing with Interaction Partners
273
Vili
Contents
4.1.3
Surface Plasmon
Resonance
274
4.2
Antibody-based
Techniques
275
A.I.I Western Blotting and Dot Blots
275
4.2.2
Protein Microarrays
276
Part II: Practical Manual of Proteome Analysis
279
Equipment, Consumables, Reagents
281
Step
1:
Sample Preparation
287
Step
2:
Fluorescence Difference Gel Electrophoresis
299
Step
3:
Isoelectric Focusing
309
Step
4:
SDS Polyacrylamide
Gel Electrophoresis
323
Step
5:
Scanning of Gels Containing Pre-labeled Proteins
357
Step
6:
Staining of Gels
361
Step
7:
Image Analysis and Evaluation of DIGE Gels
373
Step
8:
Spot Excision
383
Step
9:
Sample Destaining
387
Step
10:
Protein Digestion
389
Step
11:
Microscale Desalting and Concentrating of Sample
393
Step
12:
Chemical Derivatization of the
Peptide
Digest
397
Step
13:
MS Analysis
399
Step
14:
Calibration of MALDI-ToF MS
403
Step
15:
Preparing for a Database Search
407
Partili:
Troubleshooting
411
1
Two-dimensional Electrophoresis
413
1.1
Sample Preparation
413
1.2
Isoelectric focusing in IGPG strips
414
1.3
SDS
PAGE
416
1.4
Staining
417
Contents
I IX
1.5 DIGE
Fluorescence Labeling
418
1.6
Results in 2-D Electrophoresis
421
2
Mass Spectrometry
429
References
433
Glossary of Terms
462
Index
473
Legal Statements
481 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| author | Westermeier, Reiner 1951- Naven, Tom Höpker, Hans-Rudolf |
| author_GND | (DE-588)135840627 |
| author_facet | Westermeier, Reiner 1951- Naven, Tom Höpker, Hans-Rudolf |
| author_role | aut aut aut |
| author_sort | Westermeier, Reiner 1951- |
| author_variant | r w rw t n tn h r h hrh |
| building | Verbundindex |
| bvnumber | BV023247285 |
| classification_rvk | WC 3440 WC 4170 WC 4460 |
| classification_tum | CHE 810f CHE 808f CHE 820f BIO 220f |
| ctrlnum | (OCoLC)229442604 (DE-599)DNB986204390 |
| dewey-full | 572.636 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.636 |
| dewey-search | 572.636 |
| dewey-sort | 3572.636 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Chemie |
| discipline_str_mv | Biologie Chemie |
| edition | 2., completely rev. ed. |
| format | Book |
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| genre | (DE-588)4127380-1 Praktikum gnd-content |
| genre_facet | Praktikum |
| id | DE-604.BV023247285 |
| illustrated | Illustrated |
| index_date | 2024-07-02T20:26:24Z |
| indexdate | 2024-07-20T09:37:03Z |
| institution | BVB |
| isbn | 9783527319411 3527319417 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016432719 |
| oclc_num | 229442604 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-20 DE-19 DE-BY-UBM DE-91G DE-BY-TUM DE-1102 DE-M49 DE-BY-TUM DE-11 DE-91S DE-BY-TUM DE-188 DE-578 DE-29T DE-703 |
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| physical | XX, 482 S. zahlr. Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | Wiley-VCH |
| record_format | marc |
| spelling | Westermeier, Reiner 1951- Verfasser (DE-588)135840627 aut Proteomics in practice a guide to successful experimental design Reiner Westermeier, Tom Naven, and Hans-Rudolf Höpker 2., completely rev. ed. Weinheim Wiley-VCH 2008 XX, 482 S. zahlr. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Proteins cabt Analytical Methods cabt PAGE cabt Electrophoresis cabt Chromatogrphy cabt Spectrometry cabt Proteomanalyse (DE-588)4596545-6 gnd rswk-swf (DE-588)4127380-1 Praktikum gnd-content Proteomanalyse (DE-588)4596545-6 s DE-604 Naven, Tom Verfasser aut Höpker, Hans-Rudolf Verfasser aut text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3019253&prov=M&dok_var=1&dok_ext=htm Inhaltstext Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016432719&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Westermeier, Reiner 1951- Naven, Tom Höpker, Hans-Rudolf Proteomics in practice a guide to successful experimental design Proteins cabt Analytical Methods cabt PAGE cabt Electrophoresis cabt Chromatogrphy cabt Spectrometry cabt Proteomanalyse (DE-588)4596545-6 gnd |
| subject_GND | (DE-588)4596545-6 (DE-588)4127380-1 |
| title | Proteomics in practice a guide to successful experimental design |
| title_auth | Proteomics in practice a guide to successful experimental design |
| title_exact_search | Proteomics in practice a guide to successful experimental design |
| title_exact_search_txtP | Proteomics in practice a guide to successful experimental design |
| title_full | Proteomics in practice a guide to successful experimental design Reiner Westermeier, Tom Naven, and Hans-Rudolf Höpker |
| title_fullStr | Proteomics in practice a guide to successful experimental design Reiner Westermeier, Tom Naven, and Hans-Rudolf Höpker |
| title_full_unstemmed | Proteomics in practice a guide to successful experimental design Reiner Westermeier, Tom Naven, and Hans-Rudolf Höpker |
| title_short | Proteomics in practice |
| title_sort | proteomics in practice a guide to successful experimental design |
| title_sub | a guide to successful experimental design |
| topic | Proteins cabt Analytical Methods cabt PAGE cabt Electrophoresis cabt Chromatogrphy cabt Spectrometry cabt Proteomanalyse (DE-588)4596545-6 gnd |
| topic_facet | Proteins Analytical Methods PAGE Electrophoresis Chromatogrphy Spectrometry Proteomanalyse Praktikum |
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