Quantitative Methods in Proteomics

Part I. Planning a Proteomic Experiment 1. Important Issues in Planning a Proteomics Experiment - Statistical Considerations of Quantitative Proteomic Data Katharina Podwojski, Christian Stephan, and Martin Eisenacher Part II. Quantitative Proteomics: Gel-Based Methods 2. The Whereabouts of 2D Gels in Quantitative Proteomics Thierry Rabilloud 3. Proteome Analysis with Classical 2D-PAGE Caroline May, Frederic Brosseron, Kathy Pfeiffer, Helmut E. Meyer, and Katrin Marcus 4. Fast and Sentitive Coomassie Staining in Quantitative Proteomics Nadine Dyballa and Sabine Metzger 5. Silver Staining of 2D Electrophoresis Gels Thierry Rabilloud 6. Differential Proteome Analysis using 2D-DIGE Caroline May, Frederic Brosseron, Piotr Chartowski, Helmut E. Meyer, and Katrin Marcus Part III. Quantitative Proteomics: MS-Based Methods 7. Quantitative Mass Spectrometry-Based Proteomics: An Overview Miroslav Nikolov, Carla Schmidt, and Henning Urlaub 8. Robust Workflow for iTRAQ-Based Peptide and Protein Quantification Florian Beck, Julia Maria Burkhart, Joergt Geiger, Rene Peiman Zahedi, and Albert Sickmann 9. Relative Protein Quantification by MS/MS Using the Tandem Mass Tag Technology Loic Dayon and Jean-Charles Sanchez 10. A Rapid Approach for Isobaric Peptide Termini Labeling (Rapid-IPTL) Christian J. Koehler, Margnus O. Arntzen, Achim Treumann, and Bernd Thiede 11. ICPL - Isotope Coded Protein Label Josef Kellermann and Friedrich Lottspeich 12. Hydroponic Isotope Labeling of Entire Plants (HILEP) and High Performance Mass Spectrometry For Quantitative Plant Proteomics Laurence V. Bindschedler, Davinia J.S. Mills, and Rainer Cramer 13. In Vivo Quantitative Proteome Profiling: Planning and Evaluation of SILAC Experiments Marieluise Kirchner and Matthias Selbach 14. SILAC for the Study of Mammalian Cell Lines and Yeast Protein Complexes Heike Piechura, Silke Oeljeklaus, and Bettina Warscheid 15. Post-Digestion 18O Exchange/Labeling for Quantitative Shotgun Proteomics of Membrane Proteins Xiaoying Ye, Brian T. Luke, Donald J. Johann Jr, King C. Chan, DaRue A. Prieto, Akira Ono, Timothy D. Veenstra, and Josip Blonder 16. Application of Label Free Proteomics for Differential Analysis of Lung Carcinoma Cell Line A549 Barbara Sitek, Daniel Waldera, Gereon Poschmann, Helmut E. Meyer, and Kai Stuhler 17. Absolute Quantification (AQUA) of Proteins Using Standard Peptides and Multiple Reaction Monitoring (MRM) Carla Schmidt and Henning Urlaub 18. Absolute Multiplexed Protein Quantification Using QconCAT Technology Philip J. Brownridge, Victoria M. Harman, Deborah M. Simpson, and Robert K. Beynon 19. A Practical Guide to the FLEXIQuant Method Sasha Singh, Marc Kirchner, Judith Steen, and Hanno Steen 20. Label-Free Protein Quantitation Using Weighted Spectral Counting Christine Vogel and Edward M. Marcotte Part IV. Specific Methods - Detection and Quantification of Post-Translational Modifications 21. Discovering the Phosphoproteome of the Hydrophobic Cytochrome c Oxidase Membrane Protein Complex Stefan Helling, Maik Huttemann, Bernhard Kadenbach, Rabia Ramzan, Sebastian Vogt, and Katrin Marcus 22. Assay - A Quantitative Mass Spectrometry-Based Approach for Kinase Client Screening and Activity Analysis Yadong Huang and Jay J. Thelen 23. Robust and High-Throughput Sample Preparation for (Semi-)Quantitative Analysis of N-Glycosylation Profiles from Plasma Samples L. Renee Ruhaak, Carolin Huhn, Carolien A. M. Koeleman, Andre M. Deelder, and Manfred Wuhrer 24. Quantitative Redox Proteomics - The NOxICAT Method Claudia Lindemann and Lars I. Leichert 25. Quantitative Analysis of S-Nitrosylated Proteins Federico Torta and Angela Bachi 26. Analysis of Ubiquitinated Proteome by Quantitative Mass Spectrometry Chan Hyun Na and Junmin Peng 27. Identification of Endogenous SUMO1 Accepter Sites by Mass Spectrometry He-Hsuan Hsiao, Erick Meulmeester, and Henning Urlaub Part V. Data Analysis, Software Tools 28. Search and Decoy: the Automatic Identification of Mass Spectra Martin Eisenacher, Michael Kohl, Michael Turewicz, Markus-Hermann Koch, Julian Uszkoreit, and Christian Stephan 29. Software Tools for MS-Based Quantitative Proteomics - A Brief Overview Simone Lemeer, Hannes Hahne, Fiona Pachl, and Bernhard Kuster 30. iTRAQ Data Interpretation Marc Vaudel, Julia Maria Burkhart, Rene Peiman Zahedi, Lennart Martens, and Albert Sickmann 31. MSQuant: A Platform for Stable Isotope-Based Quantitative Proteomics Joost W. Gouw and Jeroen Krijgsveld