InflectSSP is a function that uses LC-MS data from a Thermal Proteome Profiling (TPP) experiment and user inputs to determine protein melt shifts across the proteome. There are multiple types of TPP experiments but the type that can be analyzed using this InflectSSP function is those where a single type of drug treatment or mutant cell line (Condition) is used with a single type of vehicle or wild type cell line (Control). Biological and technical replicate data sets can be analyzed by this program. These experiments also consist of those where a single gradient heat treatment (i.e. 25, 35, 40, 50, 55, 60) is used across all conditions and controls. The output of this program consists of melt curves for each protein along with summary files that include bioinformatic analysis. The output files are all saved to the Directory folder specified by the user and this is the same folder that the user saves the source input data files. The bioinformatic analysis that is generated includes overlay of melt shift data with STRING and PANTHER based annotations.
The inputs to the program consist of both MS Excel files along with user specified parameters that are used by the program to include/exclude certain data from the melt shift analysis. Inputs include the following:
The program reports the following in a folder titled “Result Files” in the Directory folder specified by the user:
The following functions are run by the InflectSSP function
library(InflectSSP) #> Registered S3 method overwritten by 'GGally': #> method from #> +.gg ggplot2