Protocol for the processing and downstream analysis of phosphoproteomic data with PhosR
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Updated: Nov 1, 2025

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors
Published on: April 29, 2022
Hani Jieun Kim1,2, Taiyun Kim1,2, Di Xiao2
1Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia.
Abstract:
Analysis of phosphoproteomic data requires advanced computational methodologies. To this end, we developed PhosR, a set of tools and methodologies implemented in R to allow the comprehensive analysis of phosphoproteomic data. PhosR enables processing steps such as imputation, normalization, and functional analysis such as kinase activity inference and signalome construction. Together, PhosR facilitates interpretation and discovery from large-scale phosphoproteomic data sets. For complete details on the use and execution of this protocol, please refer to Kim et al. (2021).
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