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Functional proteomics : methods and protocols / edited by Julie D. Thompson, Christine Schaeffer-Reiss, Marius Ueffing. — Totowa, N.J. : Humana Press, c2008. – (58.17/M592/v.484) |
Contents
Contents
Preface v
Contributors xiii
Part I: Introduction
1. A Brief Summary of the Different Types of Mass Spectrometers Used in Proteomics 3
2. Experimental Setups and Considerations to Study Microbial Interactions 17
Part II: Proteomics
3. Plant Proteomics 29
4. Methods for Human CD8~ T Lymphocyte Proteome Analysis 45
5. Label-Free Proteomics of Serum 67
6. Flow Cytometric Analysis of Cell Membrane Microparticles 79
Part II1: Protein Expression Profiling
7. Exosomes
8. Toward a Full Characterization of the Human 20S Proteasome Subunits and Their Isoforms by a Combination of Proteomic Approaches 111
9. Free-Flow Electrophoresis of the Human Urinary Proteome 131
10. Versatile Screening for Binary Protein-Protein Interactions by Yeast Two-Hybrid Mating 145
11. Native Fractionation: Isolation of Native Membrane-Bound Protein Complexes from Porcine Rod Outer Segments Using Isopycnic Density Gradient Centrifugation 161
12. Mapping of Signaling Pathways by Functional Interaction Proteomics
13. Selection of Recombinant Antibodies by Eukaryotic Ribosome Display 193
14. Production of Protein Arrays by Cell-Free Systems 207
15. Nondenaturing Mass Spectrometry to Study Noncovalent Protein/Protein and Protein/Ligand Complexes: Technical Aspects and Application to the Determination of Binding Stoichiometries 217
16. Protein Processing Characterized by a Gel-Free Proteomics Approach 245
17. Identification and Characterization of N-Glycosylated Proteins Using Proteomics 263
Part IV: Protein Analysis
18. Data Standards and Controlled Vocabularies for Proteomics 279
19. The PRIDE Proteomics Identifications Database: Data Submission， Query， and Dataset Comparison 287
20. Searching the Protein Interaction the MINT Database
21. PepSeeker: Mining Information from Proteomic Data 319
22. Toward High-Throughput and Reliable Peptide Identification via MS/MS Spectra 333
23. MassSorter: Peptide Mass Fingerprinting Data Analysis 345
24. Database Similarity Searches 361
25. Protein Multiple Sequence Alignment 379
26. Discovering Biomedical Knowledge from the Literature 415
27. Protein Subcellular Localization Prediction Using Artificial Intelligence Technology 435
28. Protein Functional Annotation by Homology 465
29. Designability and Disease 491
30. Prism: Protein-Protein Interaction Prediction by Structural Matching 505
31. Prediction of Protein Interaction Based on Similarity of Phylogenetic Trees 523
32. Large Multiprotein Structures Modeling and Simulation: The Need for Mesoscopic Models 537
33. Dynamic Pathway Modeling of Signal Transduction Networks: A Domain-Oriented Approach 559
