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

Tine 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

Íris L. Batalha and Ana Cecília 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 René 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 Taskén

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

Stephanie Munk, Jan C. Refsgaard, and Jesper V. Olsen, and Lars J. Jensen

22. Search Databases and Statistics - Pitfalls and Best Pract