Phospho-Proteomics: Methods and Protocols

ISBN-13: 9781493930487 / Angielski / Twarda / 2015 / 364 str.

Louise Von Stechow

Opis

This second edition provides up-to-date protocols focusing on techniques for the specific enrichment of phosphopeptides and phosphoproteins. Phosphoproteomics Methods and Protocols, Second Edition guides readers through different labeling strategies for quantitative phosphoproteomics; high-throughput mass spectrometry-based phosphoproteome analyses and phospho flow cytometry; and bioinformatics strategies for phosphoproteomics data analysis and integration. Additional protocols concentrate on the identification of kinase-substrate relationships by both high- and low-throughput approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.Authoritative and practical, Phosphoproteomics Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

Spis treści

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 Chromatography

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

 21. From Phosphosites to Kinases

Stephanie 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