README.md

RTSA - Ratio-based thermal shift assay analysis for cell surface thermal proteome profiling data

Description

Ratio-based thermal shift assay (RTSA) enables a more robust and sensitive detection of effects on thermal stability and in parallel on protein abundance in thermal proteome profiling data. RTSA was developed for the cell surface thermal proteome profiling (CS-TPP, Kalxdorf et al., Nature Methods, 2020).

Installation

The following installations are required:

During installation, please keep default settings.

Next, we install the RTSA package from GitHub

install.packages("devtools")

devtools::install_github("mathiaskalxdorf/RTSA")

If everything wents fine, RTSA should be installed and is ready to be used.

Usage example

An example data set is stored in the GitHub repository in the folder "Example data". Download and store this folder somewhere suitable.

With the following lines we load the RTSA package and start the analysis:

library(RTSA)
runRTSAnalysis()

A file-selection window opens. Please navigate to the downloaded folder and select the "RTSA_Analysis_config.xlsx" file. In this folder, the proteomics data should be stored as well. The file names should follow the following rules: PFC_"MSExperimentID"PF"PF-Number"QV"QV-Number"_"PNAME".txt Please check how this naming corresponds to columns in the "RTSA_Analysis_config.xlsx" file. Furthermore, please check which columns should be present in the data files for the analysis.

The analysis config file containes all configuration parameters required to run the analysis. It contains the following columns:

When analysis is done, a new subfolder will be created containing the analysis result files. The important result files are:



mathiaskalxdorf/RTSA documentation built on April 8, 2023, 9:36 p.m.