LC-Ms/MS in Proteomics: Methods and Applications

Part I: Overviews of Techniques and Approaches in LC-MS-Based Proteomics 1. Approaches and Applications of Quantitative LC-MS for Proteomics and Activitomics Pedro R. Cutillas and John F. Timms 2. Overview of Quantitative LC-MS Techniques for Proteomics and Activitomics John F. Timms and Pedro R. Cutillas 3. Instrumentation for LC-MS/MS in Proteomics Robert Chalkley 4. Bioinformatics for LC-MS/MS-Based Proteomics Richard J. Jacob 5. Analysis of Post-Translational Modifications by LC-MS/MS Hannah Johnson and Claire E. Eyers Part II: Structural Analysis of Post-Translational Modifications 6. In-Depth Analysis of Protein Phosphorylation by Multidimensional Ion Exchange Chromatography and Mass Spectrometry Maria P. Alcolea and Pedro R. Cutillas 7. Mapping of Phosphorylation Sites by LC-MS/MS Bertran Gerrits and Bernd Bodenmiller 8. Analysis of Carbohydrates on Proteins by Off-Line Normal Phase Liquid Chromatography MALDI-TOF/TOF-MS/MS Theodora Tryfona and Elaine Stephens Part III: Techniques for Quantitative LC-MS 9. Selected Reaction Monitoring Applied to Quantitative Proteomics Reiko Kiyonami and Bruno Domon 10. Basic Design of MRM Assays for Peptide Quantification Andrew James and Claus Jorgensen 11. Proteome-Wide Quantitation by SILAC Kristoffer T.G. Rigbolt and Blagoy Blagoev 12. Quantification of Proteins by iTRAQ Richard D. Unwin 13. Quantification of Proteins by Label Free LC-MS/MS Yishai Levin and Sabine Bahn Part IV: Analysis of Protein Complexes and Organelles 14. Protocol for Quantitative Proteomics of Cellular Membranes and Membrane Rafts Andrew J. Thompson and Ritchie Williamson 15. Organelle Proteomics by Label-Free and SILAC-Based Protein Correlation Profiling Joern Dengjel, Lis Jakobsen, and Jens S. Andersen 16. Mapping Protein-Protein Interactions by Quantitative Proteomics Joern Dengjel, Irina Kratchmarova, and Blagoy Blagoev Part V: Analysis of Biological Fluids and Clinical Samples 17. Analysis of Serum Proteins by LC-MS/MS Sarah Tonack, John P. Neoptolemos, and Eithne Costello 18. Urinary Proteome Profiling Using 2D-DIGE and LC-MS/MS Mark E. Weeks 19. Analysis of Peptides in Biological Fluids by LC-MS/MS Pedro R. Cutillas Part VI: Novel Applications of LC-MS 20. Quantification of Protein Kinase Activities by LC-MS Maria P. Alcolea and Pedro R. Cutillas 21. A Protocol for Top Down Proteomics Using HPLC and ETD/PTR-MS Sarah R. Hart