Proteomics today: protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology
"Over the last several years, new emphasis has been placed on the application of proteomics to perform demanding biomedical and biochemical tasks. Proteomics Today clearly describes the contributions of the latest approaches - separation techniques, modern mass spectrometry, two-dimensional ele...
Gespeichert in:
Format: | Buch |
---|---|
Sprache: | English |
Veröffentlicht: |
Hoboken, NJ
Wiley
2005
|
Schriftenreihe: | Wiley-Interscience series in mass spectrometry
|
Schlagworte: | |
Online-Zugang: | Inhaltsverzeichnis |
Zusammenfassung: | "Over the last several years, new emphasis has been placed on the application of proteomics to perform demanding biomedical and biochemical tasks. Proteomics Today clearly describes the contributions of the latest approaches - separation techniques, modern mass spectrometry, two-dimensional electrophoresis, and microarray technology - in meeting these challenges. The emerging roles of imaging mass spectrometry and protein interaction maps are also addressed." "A must-have guide for scientists and laboratory technicians who study proteins in the pharmaceutical and biotechnology industries, Proteomics Today includes helpful introductions to chapters, complete references, plus insights into future challenges. More than any other resource, Proteomics Today explains how mass spectrometry and its associated tools can turn today's proteomic research challenges into tomorrow's biomedical opportunities."--BOOK JACKET. |
Beschreibung: | XVII, 426 S. Ill., graph. Darst. |
ISBN: | 0471648175 |
Internformat
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adam_text | CONTENTS
PREFACE TO PART I XV
ACKNOWLEDGMENT XVII
I INTRODUCTION TO PART I 1
1 INSTRUMENTATION AND DEVELOPMENTS 7
1.1 Introduction / 7
1.2 Ionization Techniques for Macromolecules / 8
1.2.1 252Cf Plasma Desorption Ionization / 9
1.2.2 Fast Atom/Ion Bombardment / 10
1.2.3 Type of Fragment Ions and Nomenclature / 12
1.3 Examples on Analytical Solutions Based on
FAB MS / 12
1.3.1 Detection of Abnormalities in Hemoglobin / 13
1.3.2 Glycoprotein Structure Determination / 14
1.3.3 Early Scanning Functions on Sector
Machines / 16
1.4 Electrospray Ionization / 16
1.5 Matrix Assisted Laser Desorption Ionization / 18
1.5.1 MALDI at High Pressure / 21
vii
V lii CONTENTS
1.5.2 Desorption Ionization on Silicon (DIOS) / 21
1.5.3 Delayed Extraction / 23
1.6 Ion Detection / 24
1.6.1 MicroChannel Plates (MCPs) / 25
1.6.2 Cryogenic Detectors / 26
1.6.2.1 Superconducting Tunnel Junction / 27
1.6.2.2 Thermal Detectors / 27
1.7 Types of Analyzers / 30
1.7.1 Quadrupole Mass Filter / 30
1.7.2 Three Dimensional Quadrupole Ion Trap / 31
1.7.3 Linear Ion Trap / 32
1.7.4 Time of Flight / 34
1.7.5 Fourier Transform Ion Cyclotron Resonance / 35
1.8 Hybrid Analyzers / 38
1.8.1 Quadrupole Time of Flight / 38
1.8.2 Ion Mobility TOF / 40
1.8.3 Linear Ion Trap FT ICR / 41
1.8.4 Ion Trap TOF / 42
1.9 Tandem Mass Spectrometry / 42
1.9.1 Postsource Decay / 43
1.9.2 MS MS Measurements / 44
1.9.3 Collisional Activation / 45
1.10 Current MS Instrumentation in Proteome Analyses / 47
1.10.1 MALDI TOF / 47
1.10.2 MALDI TOF TOF / 49
1.10.3 FT ICR MS / 50
1.10.4 ION Mobility MS / 51
1.11 Current MS Based Proteomics / 52
1.11.1 Delivering Peptides to Ion Source / 53
1.11.2 Peptide Sequencing and Database Searching / 56
1.11.3 Peptide Mass Fingerprinting / 56
1.11.4 Searching with MS MS Data / 58
1.11.5 Databases for MS Data Search / 58
1.12 Recent Achievements and Future Challenges / 59
1.12.1 Current Applications / 59
1.12.2 Signal Transduction Pathways / 60
1.13 Concluding Remarks / 61
References / 63
CONTENTS iX
2 PROTEOMICS IN CANCER RESEARCH 69
2.1 Introduction / 69
2.1.1 Two Dimensional Gel Electrophoresis / 70
2.1.2 Surface Enhanced Laser Desorption Ionization / 72
2.1.3 Protein Microarrays / 73
2.1.4 Getting More Than Just Simple Change in Protein Expression / 74
2.1.5 Laser Capture Microdissection / 76
2.2 Pancreatic Ductal Adenocarcinoma / 80
2.2.1 Analyses Based on Chip Technology / 81
2.2.2 SELDI Analysis of Pancreatic Ductal Adenocarcinoma / 84
2.2.3 Protein Profiling Following Treatment with DNA
Methylation/Histone Deacetylation Inhibitors / 85
2.2.4 Proteomic Profiling of PDAC Following Treatment
with Trichostatin A / 86
2.2.5 Proteomic Profiling of PDAC Following Treatment
with 5 aza 2 deoxycytidine / 88
2.3 Proteomic Analysis of Human Breast Carcinoma / 90
2.3.1 Two DE Analysis in Breast Cancer / 91
2.3.2 Proteomic Profiling of Breast Cancer Cell Membranes / 94
2.3.3 Proteomic Analysis on Selected Tissue Samples / 96
2.4 Proteomic Profiling of Chemoresistant Cancer Cells / 97
2.4.1 Protein Alterations in Pancreas Carcinoma Cells Exposed
to Anticancer Drug / 97
2.4.2 Proteomic Profiling of Cervix Squamous Cell Carcinoma
Treated with Cisplatin / 99
2.5 Signal Pathway Profiling of Prostate Cancer / 101
2.6 Emerging Role of Functional and Activity Based Proteomics
in Disease Understanding / 103
2.7 Activity Based Protein Profiling / 105
2.8 Probing Protein Functions Using Chromophore Assisted
Laser Inactivation / 106
2.9 Role of Protein Tyrosine Kinases / 107
2.10 Concluding Remarks and Future Prospects / 109
References / 117
3 CURRENT STRATEGIES FOR PROTEIN QUANTIFICATION 127
3.1 Introduction / 127
3.1.1 Strategies Based on Labeling a Specific Amino Acid Residue / 128
3.1.2 Isotope Coded Affinity Tags / 128
X CONTENTS
3.1.3 Two Dimensional Gel Electrophoresis/MALDI TOF MS / 133
3.1.4 Labeling Lysine Residues / 137
3.1.5 Labeling Tryptophan Residues / 140
3.1.6 Methionine Containing Peptides / 141
3.2 Global Internal Standard Technology / 141
3.2.1 Acylation / 141
3.2.2 Esterification / 142
3.2.3 Incorporation of Heavy Isotopes / 143
3.3 Differential In Gel Electrophoresis / 144
3.4 Quantification of Modified Proteins / 147
3.4.1 Detection and Quantification of Phosphorylated Proteins / 148
3.4.2 Detection and Quantification of Glycosylated Proteins / 150
3.4.3 Ubiquitination / 153
3.5 Comments and Considerations / 153
3.5.1 Method of Separation / 154
3.5.2 Detection / 157
3.6 Other Approaches / 159
3.6.1 Imaging Mass Spectrometry / 159
3.6.2 Microarrays in Protein Quantification / 163
3.6.3 Protein Recognition Molecules / 164
3.6.4 Surface Chemistry / 165
3.6.5 Some Applications / 167
3.7 Emerging Role of Microfluidic Devices / 168
3.7.1 Sample Preparation and Sample Delivery / 169
3.8 Concluding Remarks / 174
References / 177
II PROTEOMICS TODAY: SEPARATION
SCIENCE AT WORK 183
4 CONVENTIONAL ISOELECTRIC FOCUSING IN GEL
MATRICES AND CAPILLARIES AND IMMOBILIZED
pH GRADIENTS 187
4.1 Introduction / 187
4.1.1 Brief Historical Survey / 188
4.2 Conventional Isoelectric Focusing in Amphoteric Buffers / 189
4.2.1 General Considerations / 189
4.2.1.1 Basic Method / 190
CONTENTS XI
4.2.1.2 Applications and Limitations / 191
4.2.1.3 Specific Advantages / 192
4.2.1 A Carrier Ampholytes / 192
4.2.2 Equipment / 194
4.2.2.1 Electrophoretic Equipment / 194
4.2.2.2 Polymerization Cassette / 195
4.2.3 Polyacrylamide Gel Matrix / 198
4.2.3.1 Reagents / 198
4.2.3.2 Gel Formulations / 200
4.2.3.3 Choice of Carrier Ampholytes / 200
4.2.4 Gel Preparation and Electrophoresis / 202
4.2.4.1 Assembling Gel Mold / 202
4.2.4.2 Filling Mold / 203
4.2.4.3 Gel Polymerization / 204
4.2.4.4 Sample Loading and Electrophoresis / 204
4.2.5 General Protein Staining / 209
4.2.5.1 Micellar Coomassie Blue G 250 / 213
4.2.5.2 Coomassie Blue R 250/CuSO4 / 213
4.2.5.3 Coomassie Blue R 250/Sulfosalicylic Acid / 213
4.2.5.4 Coomassie Blue G 250/Urea/Perchloric
Acid / 214
4.2.5.5 Silver Stain / 214
4.2.6 Specific Protein Detection Methods / 214
4.2.7 Quantitation of Focused Bands / 214
4.2.8 Troubleshooting / 216
4.2.8.1 Waviness of Bands Near Anode / 216
4.2.8.2 Burning along Cathodic Strip / 216
4.2.8.3 pH Gradients Different from Expected / 217
4.2.8.4 Sample Precipitation at Application Point / 217
4.2.9 Some Typical Applications of IEF / 218
4.2.10 Examples of Some Fractionations / 218
4.2.11 Artifacts or Not? / 222
4.3 Immobilized pH Gradients / 225
4.3.1 General Considerations / 225
4.3.1.1 Problems of Conventional IEF / 225
4.3.1.2 Immobiline Matrix / 227
4.3.1.3 Narrow and Ultranarrow pH Gradients / 230
4.3.1.4 Extended pH Gradients: General Rules for Their Generation
and Optimization / 230
Xii CONTENTS
4.3.1.5 Nonlinear, Extended pH Gradients / 232
4.3.1.6 Extremely Alkaline pH Gradients / 234
4.3.2 IPG Methodology / 235
4.3.2.1 Casting an Immobiline Gel / 235
4.3.2.2 Reswelling Dry Immobiline Gels / 237
4.3.2.3 Electrophoresis / 240
4.3.2.4 Staining and pH Measurements / 240
4.3.2.5 Storage of Immobiline Chemicals / 241
4.3.2.6 Mixed Bed CA IPG Gels / 242
4.3.3 Troubleshooting / 243
4.3.4 Some Analytical Results with IPGs / 243
4.4 Capillary Isoelectric Focusing / 247
4.4.1 General Considerations / 247
4.4.2 cIEF Methodology / 248
4.4.2.1 Increasing Resolution by Altering Slope
of pH Gradient / 249
4.4.2.2 On Problem of Protein Solubility at Their pi / 251
4.4.2.3 Assessment of pH Gradients and pi Values in cIEF / 252
4.5 Separation of Peptides and Proteins by CZE in Isoelectric Buffers / 255
4.5.1 General Properties of Amphoteric, Isoelectric Buffers / 255
4.5.2 Troubleshooting for CZE in Isoelectric Buffers / 258
4.5.3 Novel EOF Modulators / 259
4.6 Conclusions / 260
References / 261
5 SODIUM DODECYL SULFATE POLYACRYLAMIDE
GEL ELECTROPHORESIS 273
5.1 Introduction / 273
5.2 SDS Protein Complexes: a Refinement of the Model / 275
5.3 Theoretical Background of Mr Measurement by SDS PAGE / 277
5.4 Methodology / 281
5.4.1 Purity and Detection of SDS / 281
5.4.2 Molecular Mass Markers / 281
5.4.3 Prelabeling with Dyes or Fluorescent Markers / 283
5.4.4 Postelectrophoretic Detection / 285
5.4.4.1 Nondiamine, Silver Nitrate Stain / 285
5.4.4.2 Colloidal Staining / 287
5.4.4.3 Hot Coomassie Staining / 288
CONTENTS Xiii
5.4.4.4 Turbidimetric Protein Detection (Negative Stain) / 289
5.4.4.5 Negative Metal Stains / 290
5.4.4.6 Fluorescent Detection / 291
5.4.5 Possible Sources of Artifactual Protein Modification / 294
5.4.6 On Use and Properties of Surfactants / 296
5.4.7 The Use of Surfactants Other Than SDS / 300
5.4.7.1 Acid Labile Surfactants / 302
5.4.8 Anomalous Behavior / 302
5.5 Gel Casting and Buffer Systems / 303
5.5.1 Sample Pretreatment / 304
5.5.2 Standard Method Using Continuous Buffers / 306
5.5.2.1 Composition of Gels and Buffers / 307
5.5.3 Use of Discontinuous Buffers / 308
5.5.3.1 Method of Neville / 309
5.5.3.2 Method of Laemmli / 310
5.5.4 Porosity Gradient Gels / 311
5.5.5 Peptide Mapping by SDS PAGE / 314
5.5.6 SDS PAGE in Photopolymerized Gels / 318
5.5.7 Blue Native PAGE and Other Native PAGE Protocols / 321
5.6 Blotting Procedures / 322
5.6.1 Capillary and Electrophoretic Transfer / 324
5.6.2 Detection Systems after Blotting / 327
5.7 Conclusions / 331
References / 332
6 TWO DIMENSIONAL MAPS 341
6.1 Introduction / 341
6.1.1 Early Days and Evolution of 2D PAGE / 342
6.1.2 A Glimpse at Modern Times / 344
6.2 Some Basic Methodology Pertaining to 2D PAGE / 346
6.2.1 Methods of Cell Disruption / 348
6.2.2 Proteolytic Attack during Cell Disruption / 349
6.2.3 Precipitation Procedures / 351
6.2.4 Removal of Interfering Substances / 353
6.2.5 Solubilization Cocktail / 357
6.2.6 Sample Application / 365
6.2.7 Sequential Sample Extraction / 370
6.2.8 True Artifacts and Fata Morganas / 371
Xiv CONTENTS
6.3 Prefractionation Tools in Proteome Analysis / 373
6.3.1 Sample Prefractionation via Different Chromatographic
Approaches / 374
6.3.2 Sample Prefractionation via Different Electrophoretic
Techniques / 377
6.3.2.1 Rotationally Stabilized Focusing Apparatus: Rotofor / 378
6.3.2.2 Continuous Free Flow Isoelectric Focusing / 379
6.3.2.3 Continuous Free Flow Electrophoresis / 381
6.3.2.4 Gradiflow / 381
6.3.2.5 Sample Prefractionation via Multicompartment
Electrolyzers with Immobiline Membranes / 384
6.3.2.6 Off Gel IEF in Multicompartment Devices / 387
6.3.3 Prefractionation via Subcellular Organelle Purification / 388
6.3.4 Prefractionation of Membrane Proteins / 389
6.4 Multidimensional Chromatography Coupled to MS / 390
6.4.1 Eavesdropping on Thy Neighbor / 391
6.5 Protein Chips and Microarrays / 393
6.6 Nondenaturing Protein Maps / 396
6.7 Spot Matching in 2D Gels via Commercial Software / 397
6.8 Conclusions / 403
References / 405
INDEX 419
|
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id | DE-604.BV019871381 |
illustrated | Illustrated |
indexdate | 2024-07-09T20:08:03Z |
institution | BVB |
isbn | 0471648175 |
language | English |
lccn | 2004050921 |
oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-013195668 |
oclc_num | 55671520 |
open_access_boolean | |
owner | DE-M49 DE-BY-TUM DE-20 DE-11 DE-578 |
owner_facet | DE-M49 DE-BY-TUM DE-20 DE-11 DE-578 |
physical | XVII, 426 S. Ill., graph. Darst. |
publishDate | 2005 |
publishDateSearch | 2005 |
publishDateSort | 2005 |
publisher | Wiley |
record_format | marc |
series2 | Wiley-Interscience series in mass spectrometry |
spelling | Proteomics today protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology Mahmoud Hamdan ; Pier Giorgio Righetti Hoboken, NJ Wiley 2005 XVII, 426 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Wiley-Interscience series in mass spectrometry "Over the last several years, new emphasis has been placed on the application of proteomics to perform demanding biomedical and biochemical tasks. Proteomics Today clearly describes the contributions of the latest approaches - separation techniques, modern mass spectrometry, two-dimensional electrophoresis, and microarray technology - in meeting these challenges. The emerging roles of imaging mass spectrometry and protein interaction maps are also addressed." "A must-have guide for scientists and laboratory technicians who study proteins in the pharmaceutical and biotechnology industries, Proteomics Today includes helpful introductions to chapters, complete references, plus insights into future challenges. More than any other resource, Proteomics Today explains how mass spectrometry and its associated tools can turn today's proteomic research challenges into tomorrow's biomedical opportunities."--BOOK JACKET. Biologische markers gtt Eiwitten gtt Massaspectrometrie gtt Proteomen gtt Proteins Spectra Mass spectrometry Proteomics Microarray (DE-588)4544227-7 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Massenspektrometrie (DE-588)4037882-2 gnd rswk-swf Proteomanalyse (DE-588)4596545-6 gnd rswk-swf Elektrophorese (DE-588)4014373-9 gnd rswk-swf Proteomanalyse (DE-588)4596545-6 s Massenspektrometrie (DE-588)4037882-2 s Elektrophorese (DE-588)4014373-9 s Microarray (DE-588)4544227-7 s DE-604 Proteine (DE-588)4076388-2 s b DE-604 Hamdan, Mahmoud Sonstige oth Righetti, Pier Giorgio Sonstige oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013195668&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
spellingShingle | Proteomics today protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology Biologische markers gtt Eiwitten gtt Massaspectrometrie gtt Proteomen gtt Proteins Spectra Mass spectrometry Proteomics Microarray (DE-588)4544227-7 gnd Proteine (DE-588)4076388-2 gnd Massenspektrometrie (DE-588)4037882-2 gnd Proteomanalyse (DE-588)4596545-6 gnd Elektrophorese (DE-588)4014373-9 gnd |
subject_GND | (DE-588)4544227-7 (DE-588)4076388-2 (DE-588)4037882-2 (DE-588)4596545-6 (DE-588)4014373-9 |
title | Proteomics today protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology |
title_auth | Proteomics today protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology |
title_exact_search | Proteomics today protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology |
title_full | Proteomics today protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology Mahmoud Hamdan ; Pier Giorgio Righetti |
title_fullStr | Proteomics today protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology Mahmoud Hamdan ; Pier Giorgio Righetti |
title_full_unstemmed | Proteomics today protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology Mahmoud Hamdan ; Pier Giorgio Righetti |
title_short | Proteomics today |
title_sort | proteomics today protein assessment and biomarkers using mass spectrometry 2d electrophoresis and microarray technology |
title_sub | protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology |
topic | Biologische markers gtt Eiwitten gtt Massaspectrometrie gtt Proteomen gtt Proteins Spectra Mass spectrometry Proteomics Microarray (DE-588)4544227-7 gnd Proteine (DE-588)4076388-2 gnd Massenspektrometrie (DE-588)4037882-2 gnd Proteomanalyse (DE-588)4596545-6 gnd Elektrophorese (DE-588)4014373-9 gnd |
topic_facet | Biologische markers Eiwitten Massaspectrometrie Proteomen Proteins Spectra Mass spectrometry Proteomics Microarray Proteine Massenspektrometrie Proteomanalyse Elektrophorese |
url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013195668&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
work_keys_str_mv | AT hamdanmahmoud proteomicstodayproteinassessmentandbiomarkersusingmassspectrometry2delectrophoresisandmicroarraytechnology AT righettipiergiorgio proteomicstodayproteinassessmentandbiomarkersusingmassspectrometry2delectrophoresisandmicroarraytechnology |