Welcome to the PHONEMeS development page!

PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is a method to model signalling networks based on untargeted phosphoproteomics mass spectrometry data and kinase/phosphatase-substrate interactions.

This page contains the R package and accompanying scripts that implement the method (

Terfve et al. Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data., Nature Communications, 6:8033, 2015) as well as an example of how to run a PHONEMeS analysis (based on data from Wilkes et al., submitted). All of this material is unpublished and for internal use only.


This section contains the package archive for PHONEMeS (latest version, ready to be installed and used in R), as well as the scripts needed to get the raw MS data into the normalised data object needed for PHONEMeS.


This section contains the data and scripts necessary to reproduce the analysis in our manuscript, for the main data, validation data and published data, using PHONEMeS on a cluster (see how), as well as the unpublished raw data that we used.