1 Abstract

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.

2 General information

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 at: TPP and NPARC .

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

3 Installation

  1. Download the package from Bioconductor.
if (!requireNamespace("BiocManager", quietly = TRUE))

Or install the development version of the package from Github.

  1. Load the package into R session.

4 Introduction

The 2D-TPP assay is usually set up in a way that for each temperature different ligand concentrations (including a vehicle condition) are used and two adjacent temperatures each are multiplexed in a single mass spectrometry (MS) run. Typically up to 10 or 12 temperatures are used in total that add up to 5 or 6 MS runs respectively (Figure 1).