demar01/protrusionproteome: protrusionproteome

protrusionproteome package provides the infrastructure in R to automate the analysis of proteomics data derived from TMT protrusion purification proteomics experiments. It requires tabular input (i.e. proteinGroups.txt files) generated by MaxQuant software for quantitative analysis of raw mass spectrometry data. It uses SummarizedExperiments objects to handle and process high-throughput mass spectrometry data. Functions provided in the package enable filtering, og2 transformation, TMT protrusion/cell-bodies ratios calculation and median substation. It provides tools for QC checks of protrusion purification efficiency, protease efficiency and TMT incorporation. It is also includes tools for statistical testing of significantly enriched protein categories in cell protrusions.

install.packages("remotes")
remotes::install_github("demar01/protrusionproteome")