SFINX: Straightforward Filtering Index for Affinity Purification–Mass Spectrometry Data Analysis

Affinity purification–mass spectrometry is one of the most common techniques for the analysis of protein–protein interactions, but inferring bona fide interactions from the resulting data sets remains notoriously difficult. We introduce SFINX, a Straightforward Filtering INdeX that identifies true-positive protein interactions in a fast, user-friendly, and highly accurate way. SFINX outperforms alternative techniques on two benchmark data sets and is available via the Web interface at http://sfinx.ugent.be/.