Emerging technologies in protein and genomic material analysis / edited by György A. Marko-Varga and Peter L. Oroszlan.

Format:

Book

Contributor:

Marko-Varga, György A.

Oroszlan, Peter.

Series:

Journal of chromatography library 0301-4770 ; v. 68.

Journal of chromatography library, 0301-4770 ; v. 68

Language:

English

Subjects (All):

Proteins--Analysis.

Proteins.

Nucleotide sequence.

Chromatographic analysis.

Mass spectrometry.

Proteins--analysis.

Molecular Sequence Data.

Sequence Analysis, DNA.

Chromatography--methods.

Mass Spectrometry.

Medical Subjects:

Proteins--analysis.

Molecular Sequence Data.

Sequence Analysis, DNA.

Chromatography--methods.

Mass Spectrometry.

Physical Description:

xviii, 274 pages : illustrations ; 25 cm.

Edition:

First edition.

Place of Publication:

Amsterdam ; Boston : Elsevier, 2003.

Contents:

Chapter 1 Enabling Bio-analytical Technologies for Protein and Genomic Material Analysis and their Impact on Biology / Gyorgy A. Marko-Varga, Peter Oroszlan 1

1.2. Industrial impact 2

1.3. Proteomics

the new frontier after the human genome 3

1.3.1. Human proteome initiatives 3

1.3.2. Multidimensional liquid chromatography 4

1.3.3. Fast and sensitive protein sequencing by mass spectrometry 5

1.4. Protein chip arrays 6

1.5. DNA/RNA analysis 7

1.5.1. Pharmacogenomics 8

1.6. Miniaturized, micro-scale systems 8

1.6.1. Nano-sciences and nano-scale analytical systems 9

Chapter 2 DNA Sequencing: From Capillaries to Microchips / Andras Guttman 11

2.2. The early days of automated DNA sequencing 12

2.3. The advent of capillary gel electrophoresis 13

2.4. Towards higher throughput: capillary array electrophoresis 14

2.5. The promise of miniaturization: microchips 15

2.6. Dealing with the data: bioinformatics 17

Chapter 3 Phosphorprotein and Phosphoproteome Analysis by Mass Spectrometry / Mads Gronborg, Ole Norregaard Jensen 21

3.2. Phosphoprotein analysis: A challenge for mass spectrometry 22

3.3. Mass spectrometry based phosphatase/kinase assays 25

3.4. Phosphoprotein and phosphopeptide enrichment strategies 26

3.5. Chemical derivatization of phosphopeptides and phosphoproteins 27

3.6. Selective detection and sequencing of phosphopeptides by tandem mass spectrometry 27

3.7. Liquid chromatography

tandem mass spectrometry (LC-MS/MS) 29

3.8. Phosphoproteome analysis by mass spectrometry 30

3.9. Emerging MS methods for phosphoprotein analysis 31

3.10. Relative quantitation of phosphorylation site occupancy by stable isotope labeling of proteins 32

Chapter 4 Quantitative Peptide Determination Using Column-Switching Capillary Chromatography Interfaced with Mass Spectrometry / J. Abian, M. Carrascal 39

4.1.1. Capillary liquid chromatography 40

4.1.2. Interfacing LC with electrospray MS 42

4.1.3. Advantages of miniaturization in LC-MS 45

4.1.3.1 Chromatographic considerations 46

4.1.3.2 Mass spectrometric considerations 46

4.1.4. Drawbacks of capillary chromatography 49

4.1.5. The use of pre-columns and column-switching in CapLC 50

4.1.5.1 Practical advantages of PC with miniaturized LC-MS systems 51

4.1.6. Quantitative analysis 52

4.2. Instrumentation 53

4.2.1. Commercial and custom-made capLC instrumentation 53

4.2.2. Capillary column preparation 53

4.2.3. Pre-columns and column-switching 55

4.2.4. NanoESI and microESI sprayers and interfaces 55

4.2.4.1 Voltage application 56

4.2.4.2 Practical set-up 57

4.3. Examples of quantitative peptide analysis 58

4.3.1. Endothelin extraction from HUVEC 58

4.3.2. Bradykinin extraction from plasma 59

4.3.3. CapLC columns 59

4.3.4. Micro-ESI interface 60

4.3.5. CapLC-[mu]ESI MS 60

4.3.6. On-line pre-concentration (PC)-capLC-[mu]ESI MS 61

4.3.7. Matrix effects and loading capacity of the PC-capLC system 63

4.3.8. Roughness and stability of the [mu]ESI-MS interface 65

4.3.9. General performance of the analytical system 66

4.4. Resume 68

Chapter 5 On-line Continuous-flow Multi-protein Biochemical Assays for the Characterization of Bio-active Compounds Using Electrospray Quadrupole Time-of-Flight Mass Spectrometry / R.J.E. Derks, A.C. Hogenboom, H. Irth 75

5.2. Experimental 76

5.2.1. Chemicals 76

5.2.2. Continuous-flow set-up 77

5.2.3. MUX-technology set-up 78

5.2.4. Batch experiments set-up 78

5.3. Results and discussion 79

5.3.1. Optimization of MS conditions: buffers and organic modifier 80

5.3.2. MS-based bioassay: optimization with the use of batch experiments 80

5.4. On-line continuous-flow MS-based biochemical interaction 82

5.4.1. Fluorescein-biotin/streptavidin assay 82

5.4.2. Digoxin/anti-digoxigenin assay 82

5.4.3. Parallel biochemical assay 82

5.4.4. MS and MS-MS switching for identification of (bio-)active compounds in a multi-protein assay 83

5.4.5. MUX technology 85

5.7.1. Theory 90

Chapter 6 Capillary Isoelectric Focusing Developments in Protein Analysis / A. Palm 95

6.2. Detection 96

6.2.1. Imaging CIEF 96

6.2.2. Other detection methods 98

6.3. Micropreparative CIEF 103

6.4. Internal standards 104

6.5. Capillary coatings 105

6.6. CIEF applications 106

6.6.1. Protein complexes 106

6.6.2. Peptides 107

6.6.3. Recombinant proteins 107

6.6.4. Hemoglobin 113

6.6.5. Microorganisms 114

6.7. CIEF-mass spectrometry 115

6.8. Miniaturized CIEF and chip-IEF 122

6.8.1. Imaging detection 122

6.8.2. Mobilization strategies 124

6.8.3. Miscellaneous applications 125

6.8.4. Mass spectrometry 125

6.8.5. Natural pH gradients 129

Chapter 7 Bio-affinity Extraction for the Analysis of Cytokines and Proteomics Samples / Gyorgy Marko-Varga 135

7.1. Introduction to cytokine analysis 135

7.2. Capillary micro extraction linked to MALDI-TOF MS for the analysis of cytokines at femtomole levels 136

7.3. Application to the analysis of IL-8 and IL-10 in cell samples 139

7.3.1. IL-10 Analysis 140

7.3.2. Analysis of IL-8 140

7.4. Cytokine analysis conclusions 146

7.5. Sample preparation for proteomics studies 147

7.5.1. Sample preparation of cell lysates 147

7.5.2. 1D-gel analysis utilizing restricted access affinity purification 148

7.5.3. 2D-gel analysis utilizing restricted access affinity purification 149

7.6. Proteomics analysis conclusions 150

Chapter 8 Peptidomics-based Discovery of Endogenous Neuropeptides in the Brain / Per E. Andren, Marcus Svensson, Karl Skold, Per Svenningsson 155

8.1. Introduction to peptidomics 155

8.2. Peptidomics sample preparation 156

8.3. Mass spectrometry of brain tissue peptide extracts 157

8.4. Tandem mass spectrometry of endogenous neuropeptides 158

8.5. Simultaneous detection and identification of a large number of endogenous neuropeptides 158

8.6. Identification of novel neuropeptides 158

8.7. Identification of 'classical' neuropeptides 159

8.8. Identification of post-translational modifications of neuropeptides 160

8.9. Effect of microwave irradiation of brain tissue 165

Chapter 9 The Beauty of Silicon Micromachined Microstructures Interfaced to MALDI-TOF Mass Spectrometry / Thomas Laurell, Johan Nilsson, Gyorgy Marko-Varga 169

9.1. Background to miniaturization and microstructure developments within the proteomics research area 169

9.2. Introduction to microstructure technology 171

9.3. Basic concepts of protein determination 172

9.4. The benefits gained by miniaturization 174

9.4.1. Silicon microfabrication 175

9.4.2. Flow-through dispenser fabrication 176

9.4.3. Dispenser operation 178

9.5. Interfacing capillary liquid phase separations to MALDI peptide mass fingerprinting 179

9.6. Integrated on-line protein workstation 182

9.7. Integrated microanalytical tool-box components 183

9.7.1. Integrated on-chip microextraction system interfaced to peptide map fingerprinting 184

9.8. Applications to proteomic samples from high sensitivity determinations 185

9.8.1. Analyzing targeted disease cells in proteomic studies 188

9.8.2. On-line tryptic digestion sample preparation using the SMEC-microchip 188

9.9. In-vial digestion using nanovial MALDI-target arrays 191

9.9.1. Dispenser-aided nanovial digestion 192

9.9.2. High speed in-vial protein catalysis 193

9.10. Compiled platform developments 195

9.12. Future perspectives 196

Chapter 10 Identification and Characterization of Peptides and Proteins Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry / M. Palmblad, J.

Bergquist 199

10.1. On DNA and proteins 200

10.2. On body fluids as sources for clinical markers 203

10.2.1. Plasma 204

10.2.2. Cerebrospinal fluid 205

10.2.3. Saliva 205

10.2.4. Urine 206

10.3. On mass spectrometry 206

10.3.1. Ion cyclotron resonance 207

10.3.2. Fourier transform spectroscopy 209

10.3.3. Ionization techniques 210

10.4. Experimental approaches 212

10.4.1. Sample purification 213

10.4.2. Liquid chromatography 214

10.4.3. Capillary electrophoresis 214

10.4.4. Electrospray ionization 216

10.4.5. Mass spectrometry 217

10.4.6. Mass spectrometry, peptide mass fingerprinting and information 218

10.5. Proteins in mixtures and human body fluids 221

Chapter 11 Biological Single Molecule Applications and Advanced Biosensing / M. Hegner, Ch. Gerber, Y. Arntz, J. Zhang, P. Bertoncini, S. Husale, H.P. Lang, W. Grange 241

11.1.1. Macroscopic versus microscopic measurements in biology 241

11.1.2. Force sensitive methods 241

11.2. Optical tweezers 243

11.2.1. Origin of optical forces 243

11.2.2. Experimental details 244

11.2.2.1. Calibration procedure 244

11.2.2.2. State of the art instrumentation 246

11.2.2.3. Thermal noise 246

11.2.3. Recent experiments 246

11.2.3.1. Molecular motors 247

11.2.3.2. Mechanical properties of single molecules 247

11.3. Scanning force spectroscopy 248

11.3.1. Introduction to dynamic force spectroscopy 248

11.3.3. Experimental 250

11.3.4. Probability distribution and specificity of rupture forces 250

11.3.5. Dynamic measurements 251

11.3.5.1. Base pair dependence 251

11.3.5.2. Temperature dependence 252

11.3.6. Future of dynamic force spectroscopy 253

11.4. Advanced bio-sensing using micro-mechanical cantilever arrays 254

11.4.1. Introduction to micro-mechanical bio-sensors 254

11.4.2. Nanomechanical cantilever as detectors 254

11.4.3. Overview of the two detection modes 254

11.4.3.1. Static mode 254

11.4.3.2. Dynamic mode 255

11.4.4. Setups 256

11.4.5. Future applications of cantilever arrays 260.

Notes:

Includes bibliographical references and index.

ISBN:

044450964X

OCLC:

51755701

Online:

Publisher description

Table of contents