Plant Phosphoproteomics Methods and Protocols

This detailed protocol book provides phosphoproteomics techniques currently developed for use in plants, as well as offering a variety of methodologies to analyze different types of plant phosphoproteomic data. Suitable protocols for every stage of the experiment, from protein isolation and phosphopeptides enrichment to large-scale data analysis, have been considered and explored. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

1. Phosphorylation Site Motifs in Plant Protein Kinases and Their Substrates

            Lin Xi, Zhaoxia Zhang, Sandra Herold, Sarah Kassem, Xu Na Wu, and Waltraud X. Schulze

 

2. Protein Phosphorylation Response to Abiotic Stress in Plants

            Rebecca Njeri Damaris and Pingfang Yang

 

3. Protein Phosphorylation in Plant Cell Signaling

            Ping Li and Junzhong Liu

 

4. Phosphoproteomics Profiling of Receptor Kinase Mutants

            Dandan Lu, Ting Gao, Lin Xi, and Leonard Krall, and Xu Na Wu

 

5. Phosphoproteomics Analysis of Soybean Roots Under Salinity by Using the iTRAQ Labeling Approach

            Yuchen Qian, Jia Xu, and Erxu Pi

 

6. Universal Sample Preparation Workflow for Plant Phosphoproteomic Profiling

            Chuan-Chih Hsu, Justine V. Arrington, and W. Andy Tao

 

7. Mapping Plant Phosphoproteome with Improved Tandem MOAC and Label-Free Quantification

            Yanmei Chen and Xinlin Liang

 

8. SILIA-Based 4C Quantitative PTM Proteomics

            Emily Oi Ying Wong and Ning Li

 

9. Phosphoproteomics Analysis of Plant Root Tissue

            Zhe Zhu, Shubo Yang, Shalan Li, Xiaolin Yang, and Leonard Krall

 

10. Plant Phosphopeptides Enrichment by Immobilized Metal Ion Affinity Chromatography

            Xiahe Huang, Yuanya Zhang, Haitao Ge, Dandan Lu, and Yingchun Wang

 

11. Two-Dimensional Gel Electrophoresis and Pro-Q Diamond Phosphoprotein Stain-Based Plant Phosphoproteomics

            Yuan Li and Dongtao Ren

 

12. 2-D DIGE Combined with Pro-Q Diamond Staining for the Identification of Protein Phosphorylation for Chlamydomonas reinhardtii: A Successful Approach

            Li Li

 

13. Plant Phosphopeptides Identification and Label-Free Quantification by MaxQuant and Proteome Discovery Software

            Shalan Li, Haitao Zan, Zhe Zhu, Dandan Lu, and Leonard Krall

 

14. Phosphat 4.0: An Updated Arabidopsis Database for Searching Phosphorylation Sites and Kinase-Target Interactions

            Lin Xi, Zhaoxia Zhang, and Waltraud X. Schulze

 

15. Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources

            Min Zhang and Guangyou Duan

 

16. The Application of an R Language-Based Platform cRacker for Phosphoproteomics Data Analysis

            Mingjie He and Zhi Li

 

17. Kinase Activity Assay Using Unspecific Substrate or Specific Synthetic Peptides

            Jiahui Wang, Xiaolin Yang, Lin Xi, and Xu Na Wu