Note: Intro -- Proteomics in Drug Research -- Contents -- A Personal Foreword -- Preface -- List of Contributors -- I Introduction -- 1 Administrative Optimization of Proteomics Networks for Drug Development -- 1.1 Introduction -- 1.2 Tasks and Aims of Administration -- 1.3 Networking -- 1.4 Evaluation of Biomarkers -- 1.5 A Network for Proteomics in Drug Development -- 1.6 Realization of Administrative Networking: the Brain Proteome Projects -- 1.6.1 National Genome Research Network: the Human Brain Proteome Project -- 1.6.2 Human Proteome Organisation: the Brain Proteome Project -- 1.6.2.1 The Pilot Phase -- References -- 2 Proteomic Data Standardization, Deposition and Exchange -- 2.1 Introduction -- 2.2 Protein Analysis Tools -- 2.2.1 UniProt -- 2.2.2 InterPro -- 2.2.3 Proteome Analysis -- 2.2.4 International Protein Index (IPI) -- 2.2.5 Reactome -- 2.3 Data Storage and Retrieval -- 2.4 The Proteome Standards Initiative -- 2.5 General Proteomics Standards (GPS) -- 2.6 Mass Spectrometry -- 2.7 Molecular Interactions -- 2.8 Summary -- References -- II Proteomic Technologies -- 3 Difference Gel Electrophoresis (DIGE): the Next Generation of Two-Dimensional Gel Electrophoresis for Clinical Research -- 3.1 Introduction -- 3.2 Difference Gel Electrophoresis: Next Generation of Protein Detection in 2-DE -- 3.2.1 Application of CyDye DIGE Minimal Fluors (Minimal Labeling with CyDye DIGE Minimal Fluors) -- 3.2.1.1 General Procedure -- 3.2.1.2 Example of Use: Identification of Kinetic Proteome Changes upon Ligand Activation of Trk-Receptors -- 3.2.2 Application of Saturation Labeling with CyDye DIGE Saturation Fluors -- 3.2.2.1 General Procedure -- 3.2.2.2 Example of Use: Analysis of 1000 Microdissected Cells from PanIN Grades for the Identification of a New Molecular Tumor Marker Using CyDye DIGE Saturation Fluors. , 3.2.3 Statistical Aspects of Applying DIGE Proteome Analysis -- 3.2.3.1 Calibration and Normalization of Protein Expression Data -- 3.2.3.2 Detection of Differentially Expressed Proteins -- 3.2.3.3 Sample Size Determination -- 3.2.3.4 Further Applications -- References -- 4 Biological Mass Spectrometry: Basics and Drug Discovery Related Approaches -- 4.1 Introduction -- 4.2 Ionization Principles -- 4.2.1 Matrix-Assisted Laser Desorption/Ionization (MALDI) -- 4.2.2 Electrospray Ionization -- 4.3 Mass Spectrometric Instrumentation -- 4.4 Protein Identification Strategies -- 4.5 Quantitative Mass Spectrometry for Comparative and Functional Proteomics -- 4.6 Metabolic Labeling Approaches -- 4.6.1 (15)N Labeling -- 4.6.2 Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) -- 4.7 Chemical Labeling Approaches -- 4.7.1 Chemical Isotope Labeling at the Protein Level -- 4.7.2 Stable Isotope Labeling at the Peptide Level -- 4.8 Quantitative MS for Deciphering Protein-Protein Interactions -- 4.9 Conclusions -- References -- 5 Multidimensional Column Liquid Chromatography (LC) in Proteomics - Where Are We Now? -- 5.1 Introduction -- 5.2 Why Do We Need MD-LC/MS Methods? -- 5.3 Basic Aspects of Developing a MD-LC/MS Method -- 5.3.1 General -- 5.3.2 Issues to be Considered -- 5.3.3 Sample Clean-up -- 5.3.4 Choice of Phase Systems in MD-LC -- 5.3.5 Operational Aspects -- 5.3.6 State-of-the-Art - Digestion Strategy Included -- 5.3.6.1 Multidimensional LC MS Approaches -- 5.4 Applications of MD-LC Separation in Proteomics - a Brief Survey -- 5.5 Sample Clean-Up: Ways to Overcome the "Bottleneck" in Proteome Analysis -- 5.6 Summary -- References -- 6 Peptidomics Technologies and Applications in Drug Research -- 6.1 Introduction -- 6.2 Peptides in Drug Research -- 6.2.1 History of Peptide Research -- 6.2.2 Brief Biochemistry of Peptides. , 6.2.3 Peptides as Drugs -- 6.2.4 Peptides as Biomarkers -- 6.2.5 Clinical Peptidomics -- 6.3 Development of Peptidomics Technologies -- 6.3.1 Evolution of Peptide Analytical Methods -- 6.3.2 Peptidomic Profiling -- 6.3.3 Top-Down Identification of Endogenous Peptides -- 6.4 Applications of Differential Display Peptidomics -- 6.4.1 Peptidomics in Drug Development -- 6.4.2 Peptidomics Applied to in vivo Models -- 6.5 Outlook -- References -- 7 Protein Biochips in the Proteomic Field -- 7.1 Introduction -- 7.2 Technological Aspects -- 7.2.1 Protein Immobilization and Surface Chemistry -- 7.2.2 Transfer and Detection of Proteins -- 7.2.3 Chip Content -- 7.3 Applications of Protein Biochips -- 7.4 Contribution to Pharmaceutical Research and Development -- References -- 8 Current Developments for the In Vitro Characterization of Protein Interactions -- 8.1 Introduction -- 8.2 The Model System: cAMP-Dependent Protein Kinase -- 8.3 Real-time Monitoring of Interactions Using SPR Biosensors -- 8.4 ITC in Drug Design -- 8.5 Fluorescence Polarization, a Tool for High-Throughput Screening -- 8.6 AlphaScreen as a Pharmaceutical Screening Tool -- 8.7 Conclusions -- References -- 9 Molecular Networks in Morphologically Intact Cells and Tissue-Challenge for Biology and Drug Development -- 9.1 Introduction -- 9.2 A Metaphor of the Cell -- 9.3 Mapping Molecular Networks as Patterns: Theoretical Considerations -- 9.4 Imaging Cycler Robots -- 9.5 Formalization of Network Motifs as Geometric Objects -- 9.6 Gain of Functional Information: Perspectives for Drug Development -- References -- III Applications -- 10 From Target to Lead Synthesis -- 10.1 Introduction -- 10.2 Materials and Methods -- 10.2.1 Cells and Culture Conditions -- 10.2.2 In Vitro Activity Testing -- 10.2.3 Affinity Chromatography -- 10.2.4 Electrophoresis and Protein Identification. , 10.2.5 BIAcore Analysis -- 10.2.6 Synthesis of Acyl Cyanides -- 10.2.6.1 Methyl 5-cyano-5-oxopentanoate -- 10.2.6.2 Methyl 6-cyano-6-oxohexanoate -- 10.2.6.3 Methyl-5-cyano-3-methyl-5-oxopentanoate -- 10.3 Results -- 10.4 Discussion -- References -- 11 Differential Phosphoproteome Analysis in Medical Research -- 11.1 Introduction -- 11.2 Phosphoproteomics of Human Platelets -- 11.2.1 Cortactin -- 11.2.2 Myosin Regulatory Light Chain -- 11.2.3 Protein Disulfide Isomerase -- 11.3 Identification of cAMP- and cGMP-Dependent Protein Kinase Substrates in Human Platelets -- 11.4 Identification of a New Therapeutic Target for Anti-Inflammatory Therapy by Analyzing Differences in the Phosphoproteome of Wild Type and Knock Out Mice -- 11.5 Concluding Remarks and Outlook -- References -- 12 Biomarker Discovery in Renal Cell Carcinoma Applying Proteome-Based Studies in Combination with Serology -- 12.1 Introduction -- 12.1.1 Renal Cell Carcinoma -- 12.2 Rational Approaches Used for Biomarker Discovery -- 12.3 Advantages of Different Proteome-Based Technologies for the Identification of Biomarkers -- 12.4 Type of Biomarker -- 12.5 Proteome Analysis of Renal Cell Carcinoma Cell Lines and Biopsies -- 12.6 Validation of Differentially Expressed Proteins -- 12.7 Conclusions -- References -- 13 Studies of Drug Resistance Using Organelle Proteomics -- 13.1 Introduction -- 13.1.1 The Clinical Problem and the Proteomics Response -- 13.2 Objectives and Experimental Design -- 13.2.1 The Cell Lines -- 13.2.2 Organelle Isolation -- 13.2.2.1 Criteria for Isolation -- 13.2.2.2 Plasma Membrane Isolation -- 13.2.3 Protein Fractionation and Identification -- 13.2.4 Quantitative Comparisons of Protein Abundances -- 13.3 Changes in Plasma Membrane and Nuclear Proteins in MCF-7 Cells Resistant to Mitoxantrone -- References. , 14 Clinical Neuroproteomics of Human Body Fluids: CSF and Blood Assays for Early and Differential Diagnosis of Dementia -- 14.1 Introduction -- 14.2 Neurochemical Markers of Alzheimer's Disease -- 14.2.1 β-Amyloid Precursor Protein (β-APP): Metabolism and Impact on AD Diagnosis -- 14.2.2 Tau Protein and its Phosphorylated Forms -- 14.2.2.1 Hyperphosphorylation of Tau as a Pathological Event -- 14.2.2.2 Phosphorylated Tau in CSF as a Biomarker of Alzheimer's Disease -- 14.2.3 Apolipoprotein E (ApoE) Genotype -- 14.2.4 Other Possible Factors -- 14.2.5 Combined Analysis of CSF Parameters -- 14.2.6 Perspectives: Novel Techniques to Search for AD Biomarkers - Mass Spectrometry (MS), Differential Gel Electrophoresis (DIGE), and Multiplexing -- 14.3 Conclusions -- References -- 15 Proteomics in Alzheimer's Disease -- 15.1 Introduction -- 15.2 Proteomic Analysis -- 15.2.1 Sample Preparation -- 15.2.2 Two-Dimensional Electrophoresis -- 15.2.3 Protein Quantification -- 15.2.4 Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectroscopy -- 15.3 Proteins with Deranged Levels and Modifications in AD -- 15.3.1 Synaptosomal Proteins -- 15.3.2 Guidance Proteins -- 15.3.3 Signal Transduction Proteins -- 15.3.4 Oxidized Proteins -- 15.3.5 Heat Shock Proteins -- 15.3.6 Proteins Enriched in Amyloid Plaques -- 15.4 Limitations -- References -- 16 Cardiac Proteomics -- 16.1 Heart Proteomics -- 16.1.1 Heart 2-D Protein Databases -- 16.1.2 Dilated Cardiomyopathy -- 16.1.3 Animal Models of Heart Disease -- 16.1.4 Subproteomics of the Heart -- 16.1.4.1 Mitochondria -- 16.1.4.2 PKC Signal Transduction Pathways -- 16.1.5 Proteomics of Cultured Cardiac Myocytes -- 16.1.6 Proteomic Characterization of Cardiac Antigens in Heart Disease and Transplantation -- 16.1.7 Markers of Acute Allograft Rejection -- 16.2 Vessel Proteomics -- 16.2.1 Proteomics of Intact Vessels. , 16.2.2 Proteomics of Isolated Vessel Cells.