ProHits is an open source software package designed to help scientists store, search and analyze mass spectrometry data, in particular for protein-protein interaction experiments. The complete platform provides secure storage of mass spectrometry data, integration with search engines and mass spectrometry analytical tools. For more information on ProHits features, see: "ProHits: integrated software for mass spectrometry-based interaction proteomics".

ProHits Virtual Machine provides end users with a solution to analyze their affinity purification coupled to mass spectrometry data directly on their personal computer. The system is compatible with Mac OS X and Microsoft Windows, and integrated with the SAINT statistical scoring tool. To learn more about SAINT, see: "A probabilistic scoring of affinity purification-mass spectrometry data". The ProHits VM manuscript has been submitted for publication.