PhosPiR: an automated phosphoproteomic pipeline in R

Ye Hong, Dani Flinkman, Tomi Suomi, Sami Pietilä, Peter James, Eleanor Coffey, Laura L. Elo

Research output: Contribution to journalArticlepeer-review


Large-scale phosphoproteome profiling using mass spectrometry (MS) provides functional insight that is crucial for disease biology and drug discovery. However, extracting biological understanding from these data is an arduous task requiring multiple analysis platforms that are not adapted for automated high-dimensional data analysis. Here, we introduce an integrated pipeline that combines several R packages to extract high-level biological understanding from large-scale phosphoproteomic data by seamless integration with existing databases and knowledge resources. In a single run, PhosPiR provides data clean-up, fast data overview, multiple statistical testing, differential expression analysis, phosphosite annotation and translation across species, multilevel enrichment analyses, proteome-wide kinase activity and substrate mapping and network hub analysis. Data output includes graphical formats such as heatmap, box-, volcano- and circos-plots. This resource is designed to assist proteome-wide data mining of pathophysiological mechanism without a need for programming knowledge.

Original languageEnglish
Article numberbbab510
JournalBriefings in Bioinformatics
Issue number1
Publication statusPublished - 2022 Jan 1

Subject classification (UKÄ)

  • Biochemistry and Molecular Biology

Free keywords

  • Bioinformatics
  • Data visualization
  • Phosphoproteomics
  • Pipeline
  • Proteomics
  • Statistics


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