Contents

1 Abstract

Thermal proteome profiling (TPP) (Franken et al., 2015; 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 in brief monitors the profiles of proteins in cells over a temperature gradient and tries to detect shifts induced by ligand-protein interactions in a treatment versus a control sample. 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 aims at providing an analysis tool for 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: https://bioconductor.org/packages/release/bioc/html/TPP.html and https://git.embl.de/childs/TPP-data-analysis/blob/master/NPARC_paper/reports/NPARC_workflow.Rmd .

This vignette is not aimed to represent an in-depth introduction to thermal proteome profiling, please refer to other sources for this purpose:

3 Installation

  1. Download the package from Bioconductor.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TPP2D")

Or install the development version of the package from Github.

BiocManager::install(“nkurzaw/TPP2D”)
  1. Load the package into R session.
library(TPP2D)

4 Introduction

The 2D-TPP assay is usually set up in a way that for each temperature 5 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).