Affinity purification coupled to mass spectrometry (AP-MS) is now widely used for the identification of protein interaction partners in virtually all areas of biology and biomedicine. However, despite the continual advances in the sample preparation and mass spectrometric instrumentation, data management and data interpretation from the biological perspective have until recently remained major bottlenecks in interaction proteomics studies. We have developed a modular open source platform called ProHits that handles all aspects of data management, database searches and data visualization across multiple projects and multiple instruments, with administrator controlled security layers between different users and projects (Liu et al., Nature Biotech, 2010). The integration of ProHits with other open source software enables the seamless start-to-finish analysis of AP-MS experiments.
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