PeakQuant (a Proteomics software suite)
PeakQuant (formerly known as Peakardt) serves as an integrated platform for several Proteomics tools and provides an easily operated graphical user interface.
One important module is FindPairs - a generic algorithm aiming on automated quantitative analysis of isotope-labeled mass spectra with high accuracy and reliability (e.g. SILAC and 14N/15N metabolic labeling).
Other important modules are DecoyDatabaseBuilder and SetOperations, each also available as separate executables.
PeakQuant is written in Java (version 1.5.x or higher is required for Microsoft Windows, Java 1.6.x for Linux and Apple computers, 64bit versions enabling more than 3.2 GB memory are recommended!).