TPP2D analysis

This repository contains code to reproduce analyses performed by Kurzawa et al. 2020 to showcase the usage of the R package TPP2D (github) for analysis of 2D-Thermal proteome profiling experiments (2D-TPP) (Becher et al., 2016; Mateus et al., 2020).

Overview

• Panobinostat_HepG2_cell_2DTPP_Becher_et_al_2016:
  • Panobinostat_dataset_re-analysis.Rmd
  • Panobinostat_dataset_re-analysis.md
• JQ1_THP1_lysate_2DTPP_Savitski_et_al_2018:
  • JQ1_dataset_re-analysis.Rmd
  • JQ1_dataset_re-analysis.md
• PCI-34051_HL60_cell_2DTPP:
  • PCI-34051_analysis.Rmd
  • PCI-34051_analysis.md
• BRD-3811_HL60_cell_2DTPP
  • BRD-3811_analysis.Rmd
  • BRD-3811_analysis.md
• GTP_Jurkat_gelfil_lysate_2DTPP
  • GTP_analysis.Rmd
  • GTP_analysis.md
• Benchmark_on_synthetic_dataset
  • benchmark.Rmd
  • benchmark.md

References

1. Kurzawa, N. Becher, I., Sridharan, S., Franken, H., Mateus, A., Anders, S., Bantscheff, M., Huber, W. & Savitski, M., M., (2020), bioRxiv [link]
2. Becher, I., Werner, T., Doce, C., Zaal, E.A., Tögel, I., Khan, C.A., Rueger, A., Muelbaier, M., Salzer, E., Berkers, C.R., et al. (2016). Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat. Nature Chemical Biology 12, 908–910, [link]
3. Mateus, A., Kurzawa, N., Becher, I., Sridharan, S., Helm, D., Stein, F., Typas, A., and Savitski, M.M. (2020). Thermal proteome profiling for interrogating protein interactions. Molecular Systems Biology 16, e9232, [link]