Fig. 7. Proteomic analysis of PAL experiments using E. coli cell lysates.

a Western blot analysis with ExtrAvidin®-Peroxidase showing enrichment of labeled proteins under optimized conditions using PALP-2 and PALP-3 as indicated after irradiation with UV light (365 nm) for 5 min. b Heatmap representation (Z-scores) of proteins that were quantified in the respective experiments in at least four out of six measurements and that passed a one-way ANOVA-based multiple-sample test for statistically significant enrichment, with a permutation-based false discovery rate (FDR) below or equal to 0.01 and S₀ value set to 0.2, followed up by two-sided post hoc Tukey’s HSD test (FDR ≤ 0.05) to determine proteins enriched against all performed control experiments. c Venn diagram illustrating the overlap of identified proteins with PALP-3 (green) and PALP-2 (blue). d Frequencies of the enriched GO terms are compared between PALP-3 (green) and PALP-2 (blue) and the global E. coli proteome (gray) according to GO analysis using a one-sided hypergeometric test performed with the Cytoscape BiNGO resource (Supplementary Data 4). Global frequency represents the number of genes annotated to a GO term in the entire E. coli proteome, while sample frequency represents the number of genes annotated to that GO term in the protein list obtained by PAL. Source data are provided as a Source Data file.