Number of identified interprotein CSMs, ResPairs and PPIs and the empirically determined FDR at a software-defined 1% FDR cutoff using a 540-protein or 4,000-protein database and identical search parameters, including K as the only cross-linking site. Framed bars mark post hoc aggregated results, that is, cases when CSMs were aggregated to unique ResPairs or unique ResPairs to unique PPIs because search engines do not control FDR at these levels (MeroX and MaxLynx do not report FDR-controlled ResPairs; MeroX, MaxLynx, MSAnnika do not report FDR-controlled PPIs). Blue bars show true-positive identifications, yellow bars show false-positive identifications, violating the mixing scheme of our XL-MS standard.
