ISOQuant - Integrated SOlution for LC-MS based label-free protein QUANTification
I prepackaged all external libraries as JAR files in the subfolder "lib". The only additional external dependency is https://github.com/jkuharev/PLGSDataAccess.
ISOQuant and PLGSAccess are are Eclipse projects. You will need to import both into the same Eclipse workspace and then to run "isoquant.app.ISOQuant" from ISOQuant project to run the application.