Proteomics and peptidomics: new technology platforms elucidating biology
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier
2005
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| Ausgabe: | 1. ed. |
| Schriftenreihe: | Wilson & Wilson's comprehensive analytical chemistry
46 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXX, 632 S. Ill., graph. Darst. |
| ISBN: | 044451810x |
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Datensatz im Suchindex
| _version_ | 1804135340694306816 |
|---|---|
| adam_text | Titel: Proteomics and peptidomics
Autor: Marko-Varga, György A
Jahr: 2005
Contents
Contributors to Vol 46..........................................................................vii
Volumes in the Series............................................................................xi
Preface.................................................xxv
Series Editor s Preface.....................................xxix
Chapter 1. Emerging technologies—the way forward on improving
protein analysis
Gyorgy Marko-Varga
1.1 Introduction......................................................................1
1.2 The Human Proteome Organization..................................7
1.3 Pharmacogenomics............................................................11
1.4 Protein Separation and Analysis........................................14
1.4.1 Introduction......................................................14
1.4.2 Protein separation by 2D gels and liquid
chromatography................................................17
1.4.3 Alternative approaches......................................21
1.4.4 Mass spectrometry identifications......................23
1.5 Protein Annotation and Identification................................28
1.6 Biomarkers........................................................................31
1.7 Pathway Proteomics..........................................................38
1.8 Protein Chip Array Developments......................................40
1.9 Systems Biology..................................................................45
1.10 Laser Capture Microdissection and Tissue Imaging............47
1.11 Tissue Imaging and Profiling..............................................50
1.12 Conclusions........................................................................52
References....................................................................................57
Chapter 2. Capillary high-performance liquid chromatography for
proteomic and peptidomic analysis
Christian G. Huber, Christian Schley, Nathanael Delmotte
2.1 Introduction........................................................................69
2.2 Chromatographic Separation Systems for Protein and
Peptide Separations..............................................................74
xv
Contents
2 2 1 Reversed-phase and ion-pair reversed-phase
HPLC................................................................75
2.2.2 Ion-exchange chromatography............................82
2.2.3 Affinity chromatography....................................85
2.2.4 Size-exclusion chromatography..........................90
2.3 Column Technology and Stationary Phases..........................9!
2.3.1 Conventional capillary columns packed with
microparticular stationary phases......................91
2.3.2 Capillary columns for ultrahigh-pressure liquid
chromatography..................................................95
2.3.3 Monolithic capillary columns..............................98
2.4 Instrumentation for Micro- and Nanoscale Chromatography 106
2.4.1 Solvent delivery and gradient formation............108
2.4.2 Sample injection................................................113
2.4.3 Detection............................................................115
2.4.4 Instrumentation for ultrahigh-pressure liquid
chromatography..................................................119
2.5 Examples of Application......................................................122
2.5.1 Multidimensional peptide separations................122
2.5.2 Utilization of retention time information for
protein identification..........................................131
2.5.3 Identification of tumor-associated peptides..........133
2.5.4 Multidimensional analysis of intact proteins . . . 134
2.6 Conclusions and Outlook........................... 140
References.......................................... 140
Chapter 3. Peptide and protein separations by capillary electrophoresis
and electrochromatography
Akos Vegvari
3.1 Introduction................................................149
3.2 Instrumentation....................................................151
3.2.1 Equipment..................................................151
3.2.2 Detection..........................................152
3.2.3 Coatings................................................454
3.3 Electromigration Properties of Peptides and Proteins . . . . . 156
3.4 Sample Treatment..................................452
3.4.1 Preseparation and preconcentration....................162
3.4.2 Derivatization................................4gg
xv i
Contents
3.5 Capillary Electrophoresis of Peptides and Proteins..............169
3.5.1 Capillary zone electrophoresis............................170
3.5.2 Non-aqueous capillary electrophoresis ........ 178
3.5.3 Capillary gel and gel-free electrophoresis............178
3.5.4 Capillary isotachophoresis..................................182
3.5.5 Capillary isoelectric focusing..............................185
3.5.6 Micellar electrokinetic chromatography..............191
3.5.7 Affinity capillary electrophoresis........................195
3.6 Capillary Electrochromatography of Peptides and Proteins . 197
3.6.1 Open tubular capillary electrochromatography. . 198
3.6.2 Particulate capillary electrochromatography . . . 201
3.6.3 Pressure-assisted CEC (pseudo-CEC)..................209
3.7 Analytical Platforms............................................................211
3.7.1 Multidimensional separations............................211
3.7.2 Miniaturization..................................................215
3.8 Summary............................................................................217
References....................................................................................218
Chapter 4. Two-dimensional gel electrophoresis: the state of the art
Charlotte Bratt
4.1 Introduction......................................................................253
4.2 Improvements within the 2D-Page Technology..................256
4.3 Sample Preparation............................................................257
4.4 Interfering Substances........................................................258
4.5 The 2D-Page......................................................................258
4.6 Visualisation of Proteins....................................................259
4.7 Analysis of the 2D-Page......................................................260
4.8 Limitations........................................................................262
4.8.1 Dynamic range..................................................262
4.8.2 Membrane and hydrophobic proteins................263
4.8.3 Low-molecular-mass proteins............................264
4.9 Applications of Proteomics..................................................264
4.10 The Proteomic Project........................................................265
4.11 Successful Studies in the Literature using 2D-Page............267
4.12 Alternatives to 2D-Page......................................................269
4.13 Conclusion..........................................................................270
Acknowledgements........................................................................270
References....................................................................................270
xvii
Contents
Chapter 5. Phosphorylation-specific analysis strategies for mass
spectrometry: enhanced detection of phosphorylated
proteins and peptides
Allan Stensballe, Richard J. Simpson
5.1 Introduction....................................
5.1.1 Chemical properties and abundances of
phosphoamino acids...................... 277
5.1.2 Toolbox for micro-characterization of
phosphoproteins by mass spectrometry....... 278
5.2 Global Gel-Based Phosphoprotein Analysis............. 280
5.3 Neo-Classical Strategies for Phosphoprotein Analysis..... 284
5.4 Mass Spectrometry-Driven Phosphopeptide Mapping and
Sequencing..................................... 287
5.4.1 Preparation of phosphoproteins for MS analysis. 288
5.4.2 Discrimination effects and hindered detection of
phosphopeptide by mass spectrometry........ 290
5.4.3 Detection of phosphorylated peptides in peptide
mass maps............................. 294
5.4.4 Phosphorylation-specific precursor ion discovery
by MS................................ 296
5.4.5 Phosphopeptide sequencing by mass spectrometry 301
5.4.6 Nanoscale chromatography for affinity
enrichment and separation of phosphopeptide
mixtures.............................. 306
5.5 Mass Spectrometry Driven Strategies for Phosphoproteomics 316
5.5.1 Selective purification of phosphoproteins by
immunoprecipitation and affinity enrichment . . 316
5.5.2 Multidimensional protein identification
technology (MudPIT) strategy for shotgun
phosphoprotein identification............... 318
5.5.3 Ion-exchange-based separation of complex
mixtures in phosphoproteome studies........ 318
5.5.4 Affinity-based enrichment of phosphopeptides in
phosphoproteome studies.................. 319
5.5.5 Chemical derivatization strategies in
phosphoproteome studies............320
5.6 Bioinformatics Tools for Phosphoprotein Characterization,
Hypothesis-Driven Phosphoprotein Analysis and Data
Mining........................................ 321
xviii
Contents
5.7 Quantitative Strategies for Phosphoproteome Analysis .... 322
5.8 Summary............................................................................326
Acknowledgments..........................................................................327
References....................................................................................327
Chapter 6. Microtechnology principles and platforms for proteomic
analysis
Thomas Laurell, Johan Nilsson, Gyorgy Marko-Varga
6.1 Introduction........................................................................351
6.1.1 Miniaturization and microfluidics......................352
6.2 Integrated Protein Platform................................................356
6.2.1 Integrated selective enrichment target................356
6.2.2 ISET sample preparation for peptide mass
fingerprint..........................................................360
6.2.3 Application to clinical samples............................361
6.2.4 Profiling of biofluid by MALDI-MS analysis .... 362
6.2.5 In conclusion......................................................363
6.3 Proteomics Workstation Developments................................364
6.3.1 Background........................................................364
6.3.2 Autonomous sample preparation principle..........364
6.3.3 Capillary force pumped protein workstation. . . . 365
6.3.4 Development of microstructures..........................366
6.3.5 Solid-phase microextraction array......................368
6.3.6 System operation................................................368
6.3.7 Evaluation of the capillary force filling system for
sample enrichment............................................370
6.3.8 Analysis of biological samples derived from 2DGE 372
6.3.9 Conclusions........................................................375
6.4 Protein Chip Microarrays....................................................376
6.4.1 Dual-detection protein chip microarrays..............378
6.5 Conclusions and Future Perspectives....................................379
References....................................................................................380
Chapter 7. Clinical peptidomics: peptide-biomarker discovery in blood
Imke Schulte, Harald Tammen, Hartmut Selle, Hans-Dieter Zucht,
Peter Schulz-Knappe
7.1 Introduction........................................................................385
xix
Contents
7.2 Clinical Peptidomics............................................................388
7.2.1 Biomarker and drug discovery............................389
7.2.2 Clinical peptidomics............................................390
7.2.3 Peptide display methodology..............................392
7.2.4 Prerequisites for peptidomics applications in blood 399
7.2.5 Applications in pre-diabetes................................401
7.3 Outlook................................................................................404
References....................................................................................405
Chapter 8. High-resolution mass spectrometric approaches to
glycoprotein characterization
Carol L. Nilsson
8.1 Introduction.................................... 411
8.2 Glycoproteins and Mass Spectrometry................. 412
8.3 Fourier Transform Ion Cyclotron Resonance Mass
Spectrometry.................................... 414
8.4 High-Resolution Mass Spectrometric Techniques for the
Study of Glycoproteins............................ 418
8.5 Glycoproteomics: The Study of Protein Glycosylation on a
Proteome-Wide Scale.............................. 421
Acknowledgments..................................... 424
References.......................................... 424
Chapter 9. Mass spectrometry for protein identification
Fredrik Levander, Peter James
9.1 Introduction.............................................................429
9.1.1 Principle............................................................429
9.1.2 MS or MSMS?....................................................431
9.2 Mass Spectrometers............................................................432
9.3 Improving Identification......................................................434
9.3.1 Peak extraction..................................................434
9.3.2 Filtering and recalibration..................................436
9.3.3 Database search and validation..........................438
9.3.4 Settings—multiple runs......................................441
9.3.5 Complementary searches....................................441
9.4 Summary............................................................................443
References....................................................................................443
xx
v
Contents
Chapter 10. Technologies interfacing capillary electrophoresis to mass
spectrometry
Akos Vegvari, Magnus Wetterhall, Jonas Bergquist
10.1 Introduction......................................................................449
10.2 Electrospray Ionization......................................................450
10.2.1 Interfacing CE and ESI-MS............................453
10.2.2 Nanoelectrospray..............................................455
10.3 Matrix-Assisted Laser Desorption Ionization......................456
10.3.1 Interfacing CE and MALDI-MS........................459
10.4 Applications........................................................................466
10.5 Summary..........................................................................471
Acknowledgments..........................................................................472
References...................................................472
Chapter 11. Protein bioinformatics
Lars Malmstroem
11.1 Introduction......................................................................487
11.1.1 Protein function..............................................488
11.1.2 Orthologs and paralogs; homologs and analogs 490
11.1.3 Protein structure..............................................492
11.1.4 Bioinformatics...............................492
11.2 A Bioinformatical Study Exemplified..................................493
11.2.1 Sequence analysis............................................494
11.2.2 Domain and tertiary structure prediction .... 495
11.3 Summary..........................................................................497
References....................................................................................498
Chapter 12. Bioinformatics standards and tools in proteomics
Frank Potthast
12.1 Introduction....................................................................501
12.2 Data Placement................................................................503
12.3 Automated Data Placement Example: Biobeamer..............504
12.4 Data Format Standards....................................................505
12.4.1 PSI: mzData..................................................506
12.4.2 PSI: mzldent..................................................507
12.4.3 PSI-MI: molecular interactions......................509
12.4.4 mzXML..........................................................509
xxi
Contents
12.5 Search Engines; Estimation of Significance . ..........
12.6 High-Accuracy Mass Spectrometers: Composition Based
... 512
Sequencing.............................
12.7 High-Accuracy Mass Spectrometers: Peptoscope,
Automatic PTM Detection........................ 513
12.8 Other Current Developments...................... 514
12.9 Information Resources about Post-Translational
Modifications..................................
12.10 Initiatives for Proteomics Data Management—Open
Source and Commercial.......................... 515
12.11 Example of a Protein Quantification Workflow........ 516
Acknowledgments..................................... 517
References.......................................... 517
Chapter 13. Simulation as a tool for optimizing proteome analysis
Jan Eriksson, David Fenyo
13.1 Introduction......................................................................523
13.2 Developing Bases for Significance Testing..........................524
13.3 Evaluating, Comparing, and Optimizing Algorithms..........525
13.4 Predicting Success Potential of Experimental Designs .... 530
13.5 Summary.................................................532
References....................................................................................532
Chapter 14. Proteomics and remodeling of extracellular matrix in lung
diseases
Johan Malmstrom
14.1 Introduction..................................................535
14.2 Remodeling of Extracellular Matrix in Lung Diseases____ 536
14.2.1 Asthma................................................535
14.2.2 Chronic obstructive pulmonary disease
(COPD).............................. 538
14.3 The Role of Fibroblasts in Normal and Pathological
Remodeling......................................ggg
14.3.1 Fibroblast activation in wound healing...... 539
14.4 Proteome Platforms for Biological Research............ 541
14.4.1 Protein/peptide separation................ 542
14.4.2 Mass spectrometry............................543
xxii
Contents
14.4.3 Combined strategies of protein separation and
identification for biological readout..................546
14.4.4 Bioinformatics..................................................547
14.5 Proteomics Strategies in Asthma........................................548
14.5.1 Classification and disease markers....................548
14.5.2 Molecular features behind the disease and
sample complexity reduction............................550
14.6 Conclusion and Future Directions......................................551
References....................................................................................552
Chapter 15. Mammalian cell biology and proteomics
Jorge S. Burns
15.1 The Proteome is Much More Complex than the Genome . . 557
15.2 Exploring Experimental Cell Model Systems......................558
15.3 Finding Function with Selected Cells; When Less is More . 559
15.4 Sample Handling/Mishandling and Data Procurement. . . . 561
15.5 Convenient Compartments, Mining Organelles..................567
15.6 Zooming in on Modifications..............................................571
15.7 Quantitative Mass Spectrometry........................................573
15.8 The Challenge of Clinical Proteomics..................................577
15.9 Proteome Analysis of Stem Cells; Back to the Future .... 581
References....................................................................................583
Chapter 16. Clinical cancer proteomics
Ayodele Alaiya, Stig Linder
16.1 Introduction......................................................................597
16.2 On the Use of Biomarkers in tumor diagnosis....................598
16.3 Cancer Proteomics..............................................................599
16.4 Proteomics Analysis Platforms..........................................600
16.4.1 Instrumentation and technology platforms . . . 600
16.5 Protein Arrays and High-Throughput Techniques..............605
16.6 Sample Preparation Protocols............................................606
16.7 Short Overview of Applied Clinical Cancer Proteomics . . . 607
16.7.1 Differential cancer diagnosis............................609
16.7.2 Tumor grading and prognosis..........................611
16.8 Protein Profiling of Serum and other Body Fluids..............614
16.9 Future Perspectives and Challenges..................................617
xxiii
Contents
Acknowledgments..........................................................................618
References....................................................................................618
Subject Index................................................................................627
xxiv
|
| adam_txt |
Titel: Proteomics and peptidomics
Autor: Marko-Varga, György A
Jahr: 2005
Contents
Contributors to Vol 46.vii
Volumes in the Series.xi
Preface.xxv
Series Editor's Preface.xxix
Chapter 1. Emerging technologies—the way forward on improving
protein analysis
Gyorgy Marko-Varga
1.1 Introduction.1
1.2 The Human Proteome Organization.7
1.3 Pharmacogenomics.11
1.4 Protein Separation and Analysis.14
1.4.1 Introduction.14
1.4.2 Protein separation by 2D gels and liquid
chromatography.17
1.4.3 Alternative approaches.21
1.4.4 Mass spectrometry identifications.23
1.5 Protein Annotation and Identification.28
1.6 Biomarkers.31
1.7 Pathway Proteomics.38
1.8 Protein Chip Array Developments.40
1.9 Systems Biology.45
1.10 Laser Capture Microdissection and Tissue Imaging.47
1.11 Tissue Imaging and Profiling.50
1.12 Conclusions.52
References.57
Chapter 2. Capillary high-performance liquid chromatography for
proteomic and peptidomic analysis
Christian G. Huber, Christian Schley, Nathanael Delmotte
2.1 Introduction.69
2.2 Chromatographic Separation Systems for Protein and
Peptide Separations.74
xv
Contents
2 2 1 Reversed-phase and ion-pair reversed-phase
HPLC.75
2.2.2 Ion-exchange chromatography.82
2.2.3 Affinity chromatography.85
2.2.4 Size-exclusion chromatography.90
2.3 Column Technology and Stationary Phases.9!
2.3.1 Conventional capillary columns packed with
microparticular stationary phases.91
2.3.2 Capillary columns for ultrahigh-pressure liquid
chromatography.95
2.3.3 Monolithic capillary columns.98
2.4 Instrumentation for Micro- and Nanoscale Chromatography 106
2.4.1 Solvent delivery and gradient formation.108
2.4.2 Sample injection.113
2.4.3 Detection.115
2.4.4 Instrumentation for ultrahigh-pressure liquid
chromatography.119
2.5 Examples of Application.122
2.5.1 Multidimensional peptide separations.122
2.5.2 Utilization of retention time information for
protein identification.131
2.5.3 Identification of tumor-associated peptides.133
2.5.4 Multidimensional analysis of intact proteins . . . 134
2.6 Conclusions and Outlook. 140
References. 140
Chapter 3. Peptide and protein separations by capillary electrophoresis
and electrochromatography
Akos Vegvari
3.1 Introduction.149
3.2 Instrumentation.151
3.2.1 Equipment.151
3.2.2 Detection.152
3.2.3 Coatings.454
3.3 Electromigration Properties of Peptides and Proteins . . . . . 156
3.4 Sample Treatment.452
3.4.1 Preseparation and preconcentration.162
3.4.2 Derivatization.4gg
xv i
Contents
3.5 Capillary Electrophoresis of Peptides and Proteins.169
3.5.1 Capillary zone electrophoresis.170
3.5.2 Non-aqueous capillary electrophoresis . 178
3.5.3 Capillary gel and gel-free electrophoresis.178
3.5.4 Capillary isotachophoresis.182
3.5.5 Capillary isoelectric focusing.185
3.5.6 Micellar electrokinetic chromatography.191
3.5.7 Affinity capillary electrophoresis.195
3.6 Capillary Electrochromatography of Peptides and Proteins . 197
3.6.1 Open tubular capillary electrochromatography. . 198
3.6.2 Particulate capillary electrochromatography . . . 201
3.6.3 Pressure-assisted CEC (pseudo-CEC).209
3.7 Analytical Platforms.211
3.7.1 Multidimensional separations.211
3.7.2 Miniaturization.215
3.8 Summary.217
References.218
Chapter 4. Two-dimensional gel electrophoresis: the state of the art
Charlotte Bratt
4.1 Introduction.253
4.2 Improvements within the 2D-Page Technology.256
4.3 Sample Preparation.257
4.4 Interfering Substances.258
4.5 The 2D-Page.258
4.6 Visualisation of Proteins.259
4.7 Analysis of the 2D-Page.260
4.8 Limitations.262
4.8.1 Dynamic range.262
4.8.2 Membrane and hydrophobic proteins.263
4.8.3 Low-molecular-mass proteins.264
4.9 Applications of Proteomics.264
4.10 The Proteomic Project.265
4.11 Successful Studies in the Literature using 2D-Page.267
4.12 Alternatives to 2D-Page.269
4.13 Conclusion.270
Acknowledgements.270
References.270
xvii
Contents
Chapter 5. Phosphorylation-specific analysis strategies for mass
spectrometry: enhanced detection of phosphorylated
proteins and peptides
Allan Stensballe, Richard J. Simpson
5.1 Introduction.
5.1.1 Chemical properties and abundances of
phosphoamino acids. 277
5.1.2 Toolbox for micro-characterization of
phosphoproteins by mass spectrometry. 278
5.2 Global Gel-Based Phosphoprotein Analysis. 280
5.3 Neo-Classical Strategies for Phosphoprotein Analysis. 284
5.4 Mass Spectrometry-Driven Phosphopeptide Mapping and
Sequencing. 287
5.4.1 Preparation of phosphoproteins for MS analysis. 288
5.4.2 Discrimination effects and hindered detection of
phosphopeptide by mass spectrometry. 290
5.4.3 Detection of phosphorylated peptides in peptide
mass maps. 294
5.4.4 Phosphorylation-specific precursor ion discovery
by MS. 296
5.4.5 Phosphopeptide sequencing by mass spectrometry 301
5.4.6 Nanoscale chromatography for affinity
enrichment and separation of phosphopeptide
mixtures. 306
5.5 Mass Spectrometry Driven Strategies for Phosphoproteomics 316
5.5.1 Selective purification of phosphoproteins by
immunoprecipitation and affinity enrichment . . 316
5.5.2 Multidimensional protein identification
technology (MudPIT) strategy for "shotgun"
phosphoprotein identification. 318
5.5.3 Ion-exchange-based separation of complex
mixtures in phosphoproteome studies. 318
5.5.4 Affinity-based enrichment of phosphopeptides in
phosphoproteome studies. 319
5.5.5 Chemical derivatization strategies in
phosphoproteome studies.320
5.6 Bioinformatics Tools for Phosphoprotein Characterization,'
Hypothesis-Driven Phosphoprotein Analysis and Data
Mining. 321
xviii
Contents
5.7 Quantitative Strategies for Phosphoproteome Analysis . 322
5.8 Summary.326
Acknowledgments.327
References.327
Chapter 6. Microtechnology principles and platforms for proteomic
analysis
Thomas Laurell, Johan Nilsson, Gyorgy Marko-Varga
6.1 Introduction.351
6.1.1 Miniaturization and microfluidics.352
6.2 Integrated Protein Platform.356
6.2.1 Integrated selective enrichment target.356
6.2.2 ISET sample preparation for peptide mass
fingerprint.360
6.2.3 Application to clinical samples.361
6.2.4 Profiling of biofluid by MALDI-MS analysis . 362
6.2.5 In conclusion.363
6.3 Proteomics Workstation Developments.364
6.3.1 Background.364
6.3.2 Autonomous sample preparation principle.364
6.3.3 Capillary force pumped protein workstation. . . . 365
6.3.4 Development of microstructures.366
6.3.5 Solid-phase microextraction array.368
6.3.6 System operation.368
6.3.7 Evaluation of the capillary force filling system for
sample enrichment.370
6.3.8 Analysis of biological samples derived from 2DGE 372
6.3.9 Conclusions.375
6.4 Protein Chip Microarrays.376
6.4.1 Dual-detection protein chip microarrays.378
6.5 Conclusions and Future Perspectives.379
References.380
Chapter 7. Clinical peptidomics: peptide-biomarker discovery in blood
Imke Schulte, Harald Tammen, Hartmut Selle, Hans-Dieter Zucht,
Peter Schulz-Knappe
7.1 Introduction.385
xix
Contents
7.2 Clinical Peptidomics.388
7.2.1 Biomarker and drug discovery.389
7.2.2 Clinical peptidomics.390
7.2.3 Peptide display methodology.392
7.2.4 Prerequisites for peptidomics applications in blood 399
7.2.5 Applications in pre-diabetes.401
7.3 Outlook.404
References.405
Chapter 8. High-resolution mass spectrometric approaches to
glycoprotein characterization
Carol L. Nilsson
8.1 Introduction. 411
8.2 Glycoproteins and Mass Spectrometry. 412
8.3 Fourier Transform Ion Cyclotron Resonance Mass
Spectrometry. 414
8.4 High-Resolution Mass Spectrometric Techniques for the
Study of Glycoproteins. 418
8.5 Glycoproteomics: The Study of Protein Glycosylation on a
Proteome-Wide Scale. 421
Acknowledgments. 424
References. 424
Chapter 9. Mass spectrometry for protein identification
Fredrik Levander, Peter James
9.1 Introduction.429
9.1.1 Principle.429
9.1.2 MS or MSMS?.431
9.2 Mass Spectrometers.432
9.3 Improving Identification.434
9.3.1 Peak extraction.434
9.3.2 Filtering and recalibration.436
9.3.3 Database search and validation.438
9.3.4 Settings—multiple runs.441
9.3.5 Complementary searches.441
9.4 Summary.443
References.443
xx
v
Contents
Chapter 10. Technologies interfacing capillary electrophoresis to mass
spectrometry
Akos Vegvari, Magnus Wetterhall, Jonas Bergquist
10.1 Introduction.449
10.2 Electrospray Ionization.450
10.2.1 Interfacing CE and ESI-MS.453
10.2.2 Nanoelectrospray.455
10.3 Matrix-Assisted Laser Desorption Ionization.456
10.3.1 Interfacing CE and MALDI-MS.459
10.4 Applications.466
10.5 Summary.471
Acknowledgments.472
References.472
Chapter 11. Protein bioinformatics
Lars Malmstroem
11.1 Introduction.487
11.1.1 Protein function.488
11.1.2 Orthologs and paralogs; homologs and analogs 490
11.1.3 Protein structure.492
11.1.4 Bioinformatics.492
11.2 A Bioinformatical Study Exemplified.493
11.2.1 Sequence analysis.494
11.2.2 Domain and tertiary structure prediction . 495
11.3 Summary.497
References.498
Chapter 12. Bioinformatics standards and tools in proteomics
Frank Potthast
12.1 Introduction.501
12.2 Data Placement.503
12.3 Automated Data Placement Example: Biobeamer.504
12.4 Data Format Standards.505
12.4.1 PSI: mzData.506
12.4.2 PSI: mzldent.507
12.4.3 PSI-MI: molecular interactions.509
12.4.4 mzXML.509
xxi
Contents
12.5 Search Engines; Estimation of Significance . .
12.6 High-Accuracy Mass Spectrometers: Composition Based
. 512
Sequencing.
12.7 High-Accuracy Mass Spectrometers: Peptoscope,
Automatic PTM Detection. 513
12.8 Other Current Developments. 514
12.9 Information Resources about Post-Translational
Modifications.
12.10 Initiatives for Proteomics Data Management—Open
Source and Commercial. 515
12.11 Example of a Protein Quantification Workflow. 516
Acknowledgments. 517
References. 517
Chapter 13. Simulation as a tool for optimizing proteome analysis
Jan Eriksson, David Fenyo
13.1 Introduction.523
13.2 Developing Bases for Significance Testing.524
13.3 Evaluating, Comparing, and Optimizing Algorithms.525
13.4 Predicting Success Potential of Experimental Designs . 530
13.5 Summary.532
References.532
Chapter 14. Proteomics and remodeling of extracellular matrix in lung
diseases
Johan Malmstrom
14.1 Introduction.535
14.2 Remodeling of Extracellular Matrix in Lung Diseases_ 536
14.2.1 Asthma.535
14.2.2 Chronic obstructive pulmonary disease
(COPD). 538
14.3 The Role of Fibroblasts in Normal and Pathological
Remodeling.ggg
14.3.1 Fibroblast activation in wound healing. 539
14.4 Proteome Platforms for Biological Research. 541
14.4.1 Protein/peptide separation. 542
14.4.2 Mass spectrometry.543
xxii
\
Contents
14.4.3 Combined strategies of protein separation and
identification for biological readout.546
14.4.4 Bioinformatics.547
14.5 Proteomics Strategies in Asthma.548
14.5.1 Classification and disease markers.548
14.5.2 Molecular features behind the disease and
sample complexity reduction.550
14.6 Conclusion and Future Directions.551
References.552
Chapter 15. Mammalian cell biology and proteomics
Jorge S. Burns
15.1 The Proteome is Much More Complex than the Genome . . 557
15.2 Exploring Experimental Cell Model Systems.558
15.3 Finding Function with Selected Cells; When Less is More . 559
15.4 Sample Handling/Mishandling and Data Procurement. . . . 561
15.5 Convenient Compartments, Mining Organelles.567
15.6 Zooming in on Modifications.571
15.7 Quantitative Mass Spectrometry.573
15.8 The Challenge of Clinical Proteomics.577
15.9 Proteome Analysis of Stem Cells; Back to the Future . 581
References.583
Chapter 16. Clinical cancer proteomics
Ayodele Alaiya, Stig Linder
16.1 Introduction.597
16.2 On the Use of Biomarkers in tumor diagnosis.598
16.3 Cancer Proteomics.599
16.4 Proteomics Analysis Platforms.600
16.4.1 Instrumentation and technology platforms . . . 600
16.5 Protein Arrays and High-Throughput Techniques.605
16.6 Sample Preparation Protocols.606
16.7 Short Overview of Applied Clinical Cancer Proteomics . . . 607
16.7.1 Differential cancer diagnosis.609
16.7.2 Tumor grading and prognosis.611
16.8 Protein Profiling of Serum and other Body Fluids.614
16.9 Future Perspectives and Challenges.617
xxiii
Contents
Acknowledgments.618
References.618
Subject Index.627
xxiv |
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| illustrated | Illustrated |
| index_date | 2024-07-02T14:39:05Z |
| indexdate | 2024-07-09T20:38:57Z |
| institution | BVB |
| isbn | 044451810x |
| language | English |
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| spelling | Proteomics and peptidomics new technology platforms elucidating biology ed. by G. Marko-Varga 1. ed. Amsterdam [u.a.] Elsevier 2005 XXX, 632 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Wilson & Wilson's comprehensive analytical chemistry 46 Peptides Proteins Analysis Proteins analysis Proteomics Proteomanalyse (DE-588)4596545-6 gnd rswk-swf Peptide (DE-588)4045125-2 gnd rswk-swf Chemische Analyse (DE-588)4009840-0 gnd rswk-swf Proteomanalyse (DE-588)4596545-6 s DE-604 Peptide (DE-588)4045125-2 s Chemische Analyse (DE-588)4009840-0 s Marko-Varga, György Sonstige oth Wilson & Wilson's comprehensive analytical chemistry 46 (DE-604)BV000900805 46 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014788857&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Proteomics and peptidomics new technology platforms elucidating biology Wilson & Wilson's comprehensive analytical chemistry Peptides Proteins Analysis Proteins analysis Proteomics Proteomanalyse (DE-588)4596545-6 gnd Peptide (DE-588)4045125-2 gnd Chemische Analyse (DE-588)4009840-0 gnd |
| subject_GND | (DE-588)4596545-6 (DE-588)4045125-2 (DE-588)4009840-0 |
| title | Proteomics and peptidomics new technology platforms elucidating biology |
| title_auth | Proteomics and peptidomics new technology platforms elucidating biology |
| title_exact_search | Proteomics and peptidomics new technology platforms elucidating biology |
| title_exact_search_txtP | Proteomics and peptidomics new technology platforms elucidating biology |
| title_full | Proteomics and peptidomics new technology platforms elucidating biology ed. by G. Marko-Varga |
| title_fullStr | Proteomics and peptidomics new technology platforms elucidating biology ed. by G. Marko-Varga |
| title_full_unstemmed | Proteomics and peptidomics new technology platforms elucidating biology ed. by G. Marko-Varga |
| title_short | Proteomics and peptidomics |
| title_sort | proteomics and peptidomics new technology platforms elucidating biology |
| title_sub | new technology platforms elucidating biology |
| topic | Peptides Proteins Analysis Proteins analysis Proteomics Proteomanalyse (DE-588)4596545-6 gnd Peptide (DE-588)4045125-2 gnd Chemische Analyse (DE-588)4009840-0 gnd |
| topic_facet | Peptides Proteins Analysis Proteins analysis Proteomics Proteomanalyse Peptide Chemische Analyse |
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