PHONEMeS

PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry), is a method that is used to train and build large-scale Boolean logic models of signaling. PHONEMeS combines identified phosphopeptide abundance measurements (e.g., from untargeted shotgun phosphoproteomic experiments) with a large Prior Knowledge Network (PKN). The PKN is primarily built from known kinase/phosphatase-to-substrate (K/P–S) relations.

PHONEMeS is being maintained and further developed by saezlab. For more details you can check the two related publications (Terfve et.al. 2015 and Gjerga et. al. 2021) as well as it’s dedicated Github page.