SAINTexpress analysis

To assess the robustness of the statistical method (moderated t test from the limma R package) implemented in Genoppi when applied to our experimental data, we also used an alternative statistical method, SAINTexpress⁵⁶, to identify significant interaction partners of the four bait proteins in the four cell lines (Supplementary Data ⁷). For each bait in each cell line, we used the intensity data (from protein level LFQ reports) for the bait versus IgG control samples as input to run SAINTexpress, excluding contaminants and protein entries supported by < 2 unique peptides to be consistent with the filtering used for the analogous Genoppi analysis. We assessed the overlap between the significant interactors identified by Genoppi (log₂ FC > 0 and FDR ≤ 0.1) and by SAINTexpress (BFDR ≤ 0.1; Supplementary Data ⁷). On average, SAINTexpress identified more significant interactors compared to Genoppi, but ~85% of the interactors identified by Genoppi were also identified by SAINTexpress. This indicates that there is good agreement between the two methods when applied to our experimental data, and that most of the significant interaction partners we identified using Genoppi could be recapitulated using an alternative, established method.