Supplementary Figure 2: Data quality and cell envelope proteins (CEPs) recovery (coverage).

(a) Affinity-purified 290 SPA-tagged CEPs (shown in % out of 785 baits tested) from multiple biological replicates (right) of late log-phase E. coli cultures grown in rich media, and 495 baits that were subjected to AP/MS once (left) in the presence of 1 to 3 different detergents. (b-e) Number of tagged and successfully purified CEPs (based on bait recovery from MS) is plotted per compartment (log₁₀ scale; b), as well as against protein abundance (expressed in log₁₀ ppm; c), transmembrane α-helix (TMH; d-i) or ß-barrel (d-ii) and Pfam domain (e). IMPs, inner membrane proteins; OMPs, outer membrane proteins; IM, inner membrane; OM, outer membrane; PE, periplasm; LPI, inner lipoprotein; LPO, outer lipoprotein; EC, extracellular; MR, membrane-related.