Protocol for the processing and downstream analysis of phosphoproteomic data with PhosR

STAR Protoc. 2021 Jun 5;2(2):100585. doi: 10.1016/j.xpro.2021.100585. eCollection 2021 Jun 18.

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).

Keywords: Bioinformatics; Proteomics; Systems biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Phosphoproteins / chemistry*
  • Protein Kinases / metabolism
  • Proteomics / methods*
  • Signal Transduction
  • Substrate Specificity

Substances

  • Phosphoproteins
  • Protein Kinases