After .raw file processing by MaxQuant. Execute SAINTFilesCreator.R on proteinGroups.txt file to create all files required to run SAINT for interactome analysis (bait,prey and interactions).
SANIT article: https://ncbi.nlm.nih.gov/pmc/articles/PMC4102138/
Download SAINT: https://saint-apms.sourceforge.net/Main.html