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Interactive tool for Phosphoproteomics

Aaron J. Storey , Kevin Naceanceno , Renny Lan , Charity L. Washam, Lisa M. Orr , Samuel G. Mackintosh, Alan J. Tackett, Rick D. Edmondson, Zhengyu Wang, Hong-yu, Brendan Frett, Samantha Kendrick, Stephanie D. Byrum*. (2020) ProteoViz: A tool for the analysis and interactive visualization of phosphoproteomics data. Molecular Omics. DOI: 10.1039/c9mo00149b

Graphical output of motifx Sequence motif analysis

Set of R scripts for the analysis and visualization of Phosphoproteomics data sets.

Script 1: Creates metadata that links with the MaxQuant database search results
Script 2: Normalizes and runs limma differential expression on the protein lysate samples
Script 3: Normalizes phosphosites to the protein expression and runs limma differential expression
Script 4: Creates the input data file needed to run PTMsig analysis
Script 5: Runs PTMsig/ssGSEA
Script 6: Runs EGSEA gene set enrichment analysis
Script 7A-7C: Creates the interactive Shiny dashboard for visualization

MaxQuant txt files are saved in the txt folder
Scripts are in the src folder
Create a Sample_metadata.tsv and contrast_matrix.tsv file associated with your experiment to run the code


  1. M. E. Ritchie, B. Phipson, D. Wu, Y. Hu, C. W. Law, W. Shi and G. K. Smyth, Nucleic Acids Research, 2015, 43, e47-e47.

  2. K. Krug, P. Mertins, B. Zhang, P. Hornbeck, R. Raju, R. Ahmad, M. Szucs, F. Mundt, D. Forestier, J. Jane-Valbuena, H. Keshishian, M. A. Gillette, P. Tamayo, J. P. Mesirov, J. D. Jaffe, S. A. Carr and D. R. Mani, Mol Cell Proteomics, 2019, 18, 576-593.

  3. M. Alhamdoosh, C. W. Law, L. Tian, J. M. Sheridan, M. Ng and M. E. Ritchie, F1000Res, 2017, 6, 2010.


Interactive tool for Phosphoproteomics







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