Proteomics: Methods and Protocols

Part I: Introduction 1. Introduction to Proteomics Friedrich Lottspeich Part II: Electrophorestic Separations 2. High-Resolution Two-Dimensional Electrophoresis Walter Weiss and Angelika Görg 3. Non-Classical 2-D Electrophoresis Jacqueline Burré, Ilka Wittig, and Hermann Schägger 4. Protein Detection and Quantitation Technologies for Gel-Based Proteome Analysis Walter Weiss, Florian Weiland, and Angelika Görg Part III: Mass Spectrometry and Tandem Mass Spectrometry Applications 5. MALDI MS Rainer Cramer 6. Capillary Electrophoresis Coupled to Mass Spectrometry for Proteomic Profiling of Human Urine and Biomarker Discovery Petra Zürbig, Eric Schiffer, and Harald Mischak 7. A Newcomer's Guide to Nano-Liquid-Chromatography of Peptides Thomas Fröhlich and Georg J. Arnold 8. Multidimensional Protein Identification Technology (MudPIT) Katharina Lohrig and Dirk Wolters 9. Characterization of Platelet Proteins Using Peptide Centric Proteomics Oliver Simon, Stefanie Wortelkamp, and Albert Sickmann 10. Identification of the Molecular Composition of the 20S Proteasome of Mouse Intestine by High Resolution Mass Spectrometric Proteome Analysis Reinhold Weber, Regina Preywisch, Nikolay Youhnovski, Marcus Groettrup, and Michael Przybylski Part IV: Quantitative Proteomics 11. Liquid Chromatography-Mass Spectrometry-Based Quantitative Proteomics Michael W. Linscheid, Robert Ahrends, Stefan Pieper, and Andreas Kühn 12. iTRAQ-Labelling of In-Gel Digested Proteins for Relative Quantification Carla Schmidt and Henning Urlaub 13. Electrospray Mass Spectrometry for Quantitative PlasmaProteome Analysis Hong Wang and Sam Hanash Part V: Interpretation of Mass Spectrometry Data 14. Algorithms and Databases Lennart Martens and Rolf Apweiler 15. Shotgun Protein Identification and Quantification by Mass Spectrometry Bingwen Lu, Tao Xu, Robin Park, and John R. Yates III Part VI: Analysis of Protein Modifications 16. Proteomics Identification of Oxidatively Modified Proteins in Brain Rukhsana Sultana, Marzia Perluigi, and D. Allan Butterfield 17. Isotope-Labeling and Affinity Enrichment of Phosphopeptides for Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry Uma Kota, Ko-yi Chien, and Michael B. Goshe Part VII: Subcellular Proteomics 18. Organelle Proteomics: Reduction of Sample Complexity by Enzymatic In-Gel Selection of Native Proteins Veronika Reisinger and Lutz A. Eichacker 19. Isolation of Plasma Membranes from the Nervous System by Countercurrent Distribution in Aqueous Polymer Two-Phase Systems Jens Schindler and Hans Gerd Nothwang 20. Enrichment and Preparation of Plasma Membrane Proteins from Arabidopsis Thaliana for Global Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry Srijeet K. Mitra, Steven D. Clouse, and Michael B. Goshe Part VIII: Analysis of Protein Interactions 21. Tandem Affinity Purification of Protein Complexes from Mammalian Cells by the Strep/FLAG (SF)-TAP Tag Christian Johannes Gloeckner, Karsten Boldt, Annette Schumacher, and Marius Ueffing 22. Sequential Peptide Affinity (SPA) Purification System for the Systematic Isolation and Identification of Protein Complexes from Escherichia coli Mohan Babu, Gareth Butland, Oxana Pogoutse, Joyce Li, Jack F. Gre