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.
How to compile
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.