Introduction to the TPP package for analyzing Thermal Proteome Profiling data: 2D-TPP experiments

Thermal Proteome Profiling (TPP) combines the cellular thermal shift assay concept [1] with mass spectrometry based proteome-wide protein quantitation [2]. Thereby, drug-target interactions can be inferred from changes in the thermal stability of a protein upon drug binding, or upon downstream cellular regulatory events, in an unbiased manner. The package TPP facilitates this process by providing exectuable workflows that conduct all necessary data analysis steps. Recent advances in the field have lead to the development of so called 2D Thermal Proteome Profiling (2D-TPP) experiments [3]. Recent advances in the field have lead to the development of so called 2D Thermal Proteome Profiling (2D-TPP) experiments [3]. Similar as for the TPP-TR and the TPP-CCR analysis, the function analyze2DTPP executes the whole workflow from data import through normalization and curve fitting to statistical analysis. Nevertheless, all of these steps can also be invoked separately by the user. The corresponding functions can be recognized by their suffix tpp2d. Here, we first show how to start the whole analysis using analyze2DTPP. Afterwards, we demonstrate how to carry out single steps individually. For details about the analysis of 1D TRor CCR experiments [2, 4], please refer to the vignette TPP introduction 1D.