Thermal proteome profiling (TPP) (Mateus et al., 2020; Savitski et al., 2014) is an unbiased mass spectrometry-based method to assess protein-ligand interactions. It works by employing the cellular thermal shift assay (CETSA) (Molina et al., 2013) on a proteome-wide scale which monitors the profiles of proteins in cells over a temperature gradient and aims to detect shifts induced by ligand-protein interactions. 2D-TPP represents a refined version of the assay (Becher et al., 2016) which uses a concentration gradient of the ligand of interest over a temperature gradient. This package aims to analyze data retrieved from 2D-TPP experiments by a functional analysis approach.
This package implements a method to detect ligand-protein interactions from
datasets obtained with the 2D-TPP assay. Please note that methods for analyzing
convential TPP datasets (e.g. single dose, melting curve approach) can be found
This vignette is not aiming to give an in-depth introduction to thermal proteome profiling, please refer to other sources for this purpose:
Note: if you use
TPP2D in published research, please cite:
Kurzawa, N.*, Becher, I.* et al. (2020) A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles. Nat. Commun., 10.1038/s41467-020-19529-8
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("TPP2D")
Or install the development version of the package from Github.