LC-MS/MS in Proteomics: Methods and Applications

Part I: Overviews of Techniques and Approaches in LC-MS-Based Proteomics1. Approaches and Applications of Quantitative LC-MS for Proteomics and ActivitomicsPedro R. Cutillas and John F. Timms2. Overview of Quantitative LC-MS Techniques for Proteomics and ActivitomicsJohn F. Timms and Pedro R. Cutillas3. Instrumentation for LC-MS/MS in ProteomicsRobert Chalkley4. Bioinformatics for LC-MS/MS-Based ProteomicsRichard J. Jacob5. Analysis of Post-Translational Modifications by LC-MS/MSHannah Johnson and Claire E. EyersPart II: Structural Analysis of Post-Translational Modifications6. In-Depth Analysis of Protein Phosphorylation by Multidimensional Ion Exchange Chromatography and Mass SpectrometryMaria P. Alcolea and Pedro R. Cutillas7. Mapping of Phosphorylation Sites by LC-MS/MSBertran Gerrits and Bernd Bodenmiller8. Analysis of Carbohydrates on Proteins by Off-Line Normal Phase Liquid Chromatography MALDI-TOF/TOF-MS/MSTheodora Tryfona and Elaine StephensPart III: Techniques for Quantitative LC-MS9. Selected Reaction Monitoring Applied to Quantitative ProteomicsReiko Kiyonami and Bruno Domon10. Basic Design of MRM Assays for Peptide QuantificationAndrew James and Claus Jorgensen11. Proteome-Wide Quantitation by SILACKristoffer T.G. Rigbolt and Blagoy Blagoev12. Quantification of Proteins by iTRAQRichard D. Unwin13. Quantification of Proteins by Label Free LC-MS/MSYishai Levin and Sabine BahnPart IV: Analysis of Protein Complexes and Organelles14. Protocol for Quantitative Proteomics of Cellular Membranes and Membrane RaftsAndrew J. Thompson and Ritchie Williamson15. Organelle Proteomics by Label-Free and SILAC-Based Protein Correlation ProfilingJoern Dengjel, Lis Jakobsen, and Jens S. Andersen16. Mapping Protein-Protein Interactions by Quantitative ProteomicsJoern Dengjel, Irina Kratchmarova, and Blagoy BlagoevPart V: Analysis of Biological Fluids and Clinical Samples17. Analysis of Serum Proteins by LC-MS/MSSarah Tonack, John P. Neoptolemos, and Eithne Costello18. Urinary Proteome Profiling Using 2D-DIGE and LC-MS/MSMark E. Weeks19. Analysis of Peptides in Biological Fluids by LC-MS/MSPedro R. CutillasPart VI: Novel Applications of LC-MS20. Quantification of Protein Kinase Activities by LC-MSMaria P. Alcolea and Pedro R. Cutillas21. A Protocol for Top Down Proteomics Using HPLC and ETD/PTR-MSSarah R. Hart