Part I: Introduction 1. Survey of Shotgun Proteomics Fabio Cesar Sousa Nogueira and Gilberto B. Domont Part II: Sample Pre-Fractionation 2. LC-MALDI-TOF/TOF for Shotgun Proteomics Patricia Fernandez-Puente, Jesus Mateos, Francisco J. Blanco and Cristina Ruiz-Romero 3. Fully Automatable Multidimensional Reversed-Phase Liquid Chromatography with Online Tandem Mass Spectrometry Maggie P.Y. Lam, Henry Law, Quan Quan, Yun Zhao, and Ivan K. Chu 4. GeLC-MS/MS Analysis of Complex Protein Mixtures Monika Dzieciatkowska, Ryan Hill, and Kirk C. Hansen 5. IPG Strip-Based Peptide Fractionation for Shotgun Proteomics Murat Eravci, Christian Sommer and Matthias Selbach Part III: In Vivo Stable Isotope Labeling 6. SILAC Yeast: From Labeling to Comprehensive Proteome Quantification Lyris M.F. de Godoy 7. Analysis of Proteome Dynamics in Mice by Isotopic Labeling John C. Price and Sina Ghaemmaghami 8. Stable Isotope Labeling in Mammals (SILAM) Daniel B. McClatchy and John R. Yates III 9. Analysis of Individual Protein Turnover in Live Animals on a Proteome-Wide Scale Stefan Reckow and Christian Webhofer Part IV: In Vitro Stable Isotope Labeling 10. Determining Protein Subcellular Localization in Mammalian Cell Culture with Biochemical Fractionation and iTRAQ 8-Plex Quantification Andy Christoforou, Alfonso Martinez Arias and Kathryn S. Lilley 11. Brain Quantitative Proteomics Combining GeLC-MS and Isotope-Coded Protein Labeling (ICPL) Giuseppina Maccarrone, Maria Lebar and Daniel Martins-de-Souza 12. Employing TMT Quantification in a Shotgun-MS Platform Darragh P. O'Brien and John F. Timms 13. Employing TMT Quantification in Shotgun-MS Proteomic Analysis: A Focus on Skeletal Muscle Bruno Menezes de Oliveira Part V: Label-Free Proteomics 14. Spectral Counting Label-Free Proteomics Liisa Arike and Lauri Peil 15. Quantification of Proteins by Label Free LC-MSE Alon Savidor and Yishai Levin Part VI: Proteomics Informatics and Quantitation 16. Bioinformatics for Proteomics: Opportunities at the Interface Between the Scientists, Their Experiments and the Community Marc Vaudel, Harald Barsnes, Lennart Martens and Frode S. Berven Part VII: Protein-Protein Interactions 17. Identification of DNA Damage Checkpoint-Dependent Protein Interactions in Saccharomyces cerevisiae Using Quantitative Mass Spectrometry Francisco M. Bastos de Oliveira and Marcus B. Smolka 18. Application of Shotgun Proteomics for Discovery-Driven Protein-Protein Interaction Livia Goto-Silva, Zoltan Maliga, Mikolaj Slabicki, Jimmy Rodriguez Murillo and Magno Junqueira 19. Mapping Protein Complexes Using Covalently Linked Antibodies and Isobaric Mass Tags Antje Dittmann, Sonja Ghidelli-Disse, Carsten Hopf and Marcus Bantscheff Part VIII: Targeted Proteomics 20. Biomarker Verification Using Selected Reaction Monitoring and Shotgun Proteomics Angel Mauricio Castro-Gamero, Clarice Izumi, and Jose Cesar Rosa 21. Use of Universal Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-Based Selected Reaction Monitoring (SRM) Approach for Verification of Breast Cancer-Related Protein Markers Ning Qing Liu, Lennard J.M. Dekker, Martijn M. Van Duijn, and Arzu Umar 22. The Secretome Analysis by High Throughput Proteomics and Multiple Reaction Monitoring (MRM) Vitor M. Faca, Camila S. Palma, Daniele Albuquerque, Gabriela N. S. Canchaya, Mariana L. Grassi, Vera L. Epifanio and Eduardo B. de Oliveira 23. Preparation of Heteroelement-Incorporated and Stable Isotope-Labeled Protein Standards for Quantitative Proteomics Anna Konopka, Nico Zinn, Christina Wild and Wolf D. Lehmann Part IX: Post-Translational Modifications 24. One-Source Peptide/Phosphopeptide Ratio Standards for Accurate and Site-Specific Determination of the Degree of Phosphorylation Martin E. Boehm, Bettina Hahn and Wolf D. Lehmann 25. Quantitative Glycoproteomics for N-Glycoproteome Profiling Sheng Pan 26. A Practical Recipe to Survey Phosphoproteomes William C. Edelman, Kelsey M. Haas, Joanne I. Hsu, Robert T. Lawrence and Judit Villen 27. Quantitation of the Phosphoproteome Using the Library Assisted eXtracted Ion Chromatogram (LAXIC) Strategy Justine V. Arrington, Liang Xue and W. Andy Tao 28. Fast, Efficient, and Quality-Controlled Phosphopeptide Enrichment from Minute Sample Amounts Using Titanium Dioxide Clarissa Dickhut, Sonja Radau and Rene P. Zahedi 29. Quantifying Small Molecule-Induced Changes in Cellular Protein Expression and Post-Translational Modifications Using Isobaric Mass Tags Isabelle Becher, Maria Falth Savitski, and Marcus Bantscheff Part X: Mass Spectrometry for Protein Analysis 30. Analysis of Protein Structure by Crosslinking Combined with Mass Spectrometry Evgeniy V. Petrotchenko, Karl A.T. Makepeace, Jason J. Serpa and Christoph H. Borchers 31. Top Down Proteomics by Means of Orbitrap Mass Spectrometry Kai Scheffler
