Kinase Signaling Networks, 1st ed. 2017 Methods in Molecular Biology Series, Vol. 1636

1. Optogenetic Control of Ras/Erk Signaling Using the Phy–PIF System

            Alexander G. Goglia, Maxwell Z. Wilson, Daniel B. DiGiorno, and Jared E. Toettcher

2. Dissecting Kinase Effector Signaling Using the RapRTAP Methodology

            Anne-Marie Ray, Jennifer E. Brinks-Klomp, Kerrie B. Collins, and Andrei V. Karginov

            Michael Pargett, Taryn E. Gillies, Carolyn K. Teragawa, Breanne Sparta, and John G. Albeck

4. Quantification of Cell Signaling Networks Using Kinase Activity Chemosensors

            Jon R. Beck, Edward N. Harris, and Cliff I. Stains

5. Expression of Recombinant Phosphoproteins for Signal Transduction Studies

6. Allosteric Modulation of Src-Family Kinases with ATP-Competitive Inhibitors

            Ames C. Register, Sujata Chakraborty, and Dustin J. Maly

7. Characterization of Ligand Binding to Pseudokinases Using a Thermal Shift Assay

            Isabelle S. Lucet and James M. Murphy

8. Proteomic Profiling of Protein Kinase Inhibitor Targets by Mass Spectrometry

9. Utilizing the Luminex Magnetic Bead-Based Suspension Arrays for Rapid Multiplexed Phosphoprotein Quantification

            Adam Stewart and Udai Banerji

10. High-Content Imaging and RNAi Screens for Investigating Kinase Network Plasticity

            Simon R. Stockwell and Sibylle Mittnacht

11. Analysis of Drug Resistance Using Kinome-Wide Functional Screens

            Katherine R. Singleton, Keith T. Earley, and Lynn E. Heasley

12. Identification and Validation of Driver Kinases from Next Generation Sequencing Data

            Andri Leonidou, Barrie Peck, and Rachael Natrajan

Part II: Mass Spectrometry and Metabolic Analysis of Kinase Signaling

13. Label-Free Phosphoproteomic Approach for Kinase Signaling Analysis

            Edmund Wilkes and Pedro R. Cutillas

14. Cell-Specific Labeling for Analyzing Bidirectional Signaling by Mass Spectrometry

            Christopher J. Tape and Claus Jørgensen

15. Characterization of the Phospho-Adhesome by Mass Spectrometry-Based Proteomics

16. Analysis of Phosphotyrosine Signaling Networks in Lung Cancer Cell Lines

            Malgorzata Broncel and Paul H. Huang

17. Targeted Analysis of Phosphotyrosine Signaling by Multiple-Reaction-Monitoring Mass Spectrometry

            Leo S. Payne and Paul H. Huang

18. Phosphoproteomic Analysis of Isolated Mitochondria in Yeast

            Margaux Renvoisé, Ludovic Bonhomme, Marlène Davanture, Michel Zivy, and Claire Lemaire

19. A Methodology for Comprehensive Analysis of Toll-Like Receptor Signaling in Macrophages

            Marijke Koppenol-Raab and Aleksandra Nita-Lazar

20. Absolute Phosphorylation Stoichiometry Analysis by Motif-Targeting Quantitative Mass Spectrometry

            Chia-Feng Tsai, Wei-Chi Ku, Yu-Ju Chen, and Yasushi Ishihama

21. Identification of Plant Kinase Substrates Based on Kinase Assay-Linked Phosphoproteomics

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

22. Mass Spectrometry Analysis of Spatial Protein Networks by Colocalization Analysis (COLA)

            Faraz K. Mardakheh

23. Development of Selected Reaction Monitoring Methods to Systematically Quantify Kinase Abundance and Phosphorylation Stoichiometry in Human Samples

            Kirsten Beck, Nathan Camp,  Michael Bereman, James Bollinger, Jarrett Egertson, Michael MacCoss, and Alejandro Wolf-Yadlin

24. Analysis of Signaling Networks at the Single Cell Level Using Mass Cytometry

            Shovik Bandyopadhyay, Daniel A.C. Fisher, Olga Malkova, and Stephen T. Oh

25. Magnetic Resonance Spectroscopy (MRS)-Based Methods for Examining Cancer Metabolism in Response to Oncogenic Kinases Drug Treatment

            Yuen-Li Chung

26. Deconstructing the Metabolic Networks of Oncogenic Signaling Using Targeted Liquid-Chromatography Tandem Mass Spectrometry (LC-MS/MS)

            George Poulogiannis

Part III: Computational Analysis of Kinase Signaling Networks

27. Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols

28. An Interdisciplinary Approach for Designing Kinetic Models of the Ras/MAPK Signaling Pathway

            Marcelo S. Reis, Vincent Noël, Matheus H. Dias, Layra L. Albuquerque, Amanda S. Guimarães, Lulu Wu, Junior Barrera, and Hugo A. Armelin

29. Databases and Computational Tools for Evolutionary Analysis of Protein Phosphorylation

            Chris Tan Soon Heng

30. Informatics Approaches for Predicting, Understanding, and Testing Cancer Drug Combinations

            Jing Tang

31. Target Inhibition Maps Based on Responses to Kinase Inhibitors

            Noah Berlow and Ranadip Pal

32. Partial Least Squares Regression Models for the Analysis of Kinase Signaling

            Danielle L. Bourgeois and Pamela K. Kreeger

Includes cutting-edge techniques for the study of kinase signaling networks

Provides step-by-step detail essential for reproducible results

Contains key implementation advice from the experts

Includes supplementary material: sn.pub/extras

Includes supplementary material: sn.pub/extras