Phospho-proteomics : methods and protocols

Part I: Techniques for Tagging Phospho-Moieties 1. Thiol-ene Enabled Detection of Thiophosphorylation as a Labeling Strategy for Phosphoproteins Kaelyn E. Wilke and Erin E. Carlson 2. Phosphopeptide Detection with Biotin-Labeled Phos-tag Emiko Kinoshita-Kikuta, Eiji Kinoshita and Tohru Koike 3. Phosphopeptide Enrichment by Covalent Chromatography after Solid Phase Derivatization of Protein Digests on Reversed Phase Supports Heinz Nika, Ruth Hogue Angeletti, and David H. Hawke Part II: Labeling Techniques for Quantitative Phosphoproteomics 4. Peptide Labeling Using Isobaric Tagging Reagents for Quantitative Phosphoproteomics Lei Cheng, Trairak Pisitkun, Mark A. Knepper, and Jason D. Hoffert 5. Identification of Direct Kinase Substrates Using Analogue-Sensitive Alleles Daniel A. Rothenberg, Elizabeth A. Gordon, Forest M. White, and Sebastian Lourido 6. Quantitative Analysis of Tissue Samples by Combining iTRAQ Isobaric Labeling with Selected/Multiple Reaction Monitoring (SRM/MRM) Ryohei Narumi and Takeshi Tomonaga Part III: Phosphopeptide Enrichment Strategies 7. Enrichment Strategies in Phosphoproteomics Alexander Leitner 8. Phosphopeptide Enrichment by Immobilized Metal Affinity ChromatographyTine E. Thingholm and Martin R. Larsen 9. The use of Titanium Dioxide for Selective Enrichment of Phosphorylated Peptides Tine E. Thingholm and Martin R. Larsen 10. Sequential Elution from IMAC (SIMAC) - An Efficient Method for Enrichment and Separation of Mono- and Multi-Phosphorylated Peptides Tine E. Thingholm and Martin R. Larsen 11. Improving the Phosphoproteome Coverage for Limited Sample Amounts Using TiO2-SIMAC-HILIC (TiSH) Phosphopeptide Enrichment and Fractionation Kasper Engholm-Keller and Martin R. Larsen 12. Offline High pH Reversed-Phase Peptide Fractionation for Deep Phosphoproteome Coverage Tanveer S Batth, Jesper V Olsen 13. Phosphopeptide Enrichment Using Various Magnetic Nanocomposites - An Overview Iris L. Batalha and Ana Cecilia A. Roque Part IV: Phosphoprotein Analysis by Mass Spectrometry 14. Two Dimensional Gel Electrophoresis-Based Plant Phosphoproteomics Chao Han and Pingfang Yang 15. Variable Digestion Strategies for Phosphoproteomics Analysis Humberto Gonczarowska-Jorge, Margherita Dell'Aica, Clarissa Dickhut, and Rene P. Zahedi 16. On-line LC-FAIMS-MS/MS for the Analysis of Phosphorylation in Proteins Hongyan Zhao, Andrew J. Creese, and Helen J. Cooper 17. Simple and Reproducible Sample Preparation for Single Shot Phosphoproteomics With High Sensitivity Rosa R. Jersie-Christensen, Abida Sultan, and Jesper V. Olsen Part V: High-throughput Studies of the Phosphoproteome 18. Identification of Direct Kinase Substrates via Kinase Assay Linked Phosphoproteomics Liang Xue, Justine V. Arrington, and W. Andy Tao 19. Phosphoprotein Detection by High-Throughput Flow Cytometry Johannes Landskron and Kjetil Tasken Part VI: Bioinformatics Resources for Phosphoproteomics Analyses 20. Resources for Assignment of Phosphorylation Sites on Peptides and Proteins Vaishnavi Ravikumar, Boris Macek, and Ivan Mijakovic 21. From Phosphosites to KinasesStephanie Munk, Jan C. Refsgaard, and Jesper V. Olsen, and Lars J. Jensen 22. Search Databases and Statistics - Pitfalls and Best Practices in Phosphoproteomics Jan C. Refsgaard, Stephanie Munk, and Lars J. Jensen 23. Systems Analysis for Interpretation of Phosphoproteomics Data Stephanie Munk, Jan C. Refsgaard, and Jesper V. Olsen