LC-MS/MS in Proteomics, Softcover reprint of the original 1st ed. 2010
Methods and Applications
Methods in Molecular Biology Series, Vol. 658

With the development of new quantitative strategies and powerful bioinformatics tools to cope with the analysis of the large amounts of data generated in proteomics experiments, liquid chromatography with tandem mass spectrometry (LC-MS/MS) is making possible the analysis of proteins on a global scale, meaning that proteomics can now start competing with cDNA microarrays for the analysis of whole genomes. In LC-MS/MS in Proteomics: Methods and Applications, experts in the field provide protocols and up-to-date reviews of the applications of LC-MS/MS, with a particular focus on MS-based methods of protein and peptide quantification and the analysis of post-translational modifications. Beginning with overviews of the use of LC-M/MS in protein analysis, the book continues with topics such as protocols for the analysis of post-translational modifications, with particular focus on phosphorylation and glycosylation, popular techniques for quantitative proteomics, such as multiple reaction monitoring, metabolic labelling, and chemical tagging, biomarker discovery in biological fluids, as well as novel applications of LC-MS/MS. Written in the highly successful Methods in Molecular Biology? series format, chapters include introductions to their respective subjects, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, LC-MS/MS in Proteomics: Methods and Applications presents the techniques and concepts necessary in order to aid proteomic practitioners in the application of LC-MS/MS to essentially any biological problem.

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