Extended Data Fig. 4: Characterization of TME binders in the tunicamycin dataset.
From: Global analysis of endogenous protein disorder in cells
a, Strategies to interpret proteomics results. In each dataset, there were four experimental conditions: TME-/Drug-, TME + /Drug-, TME-/Drug + , TME + /Drug + . Each experimental condition was processed parallelly with the RUBICON workflow. Note that unlabeled proteins can be potentially enriched by Dynabeads, that is, non-specific binders. Comparison of TME-/Drug- and TME + /Drug- identified TME binders in control condition, for example, Fig. 3a. Comparison of TME-/Drug+ and TME + /Drug+ identified TME binders in drug treated conditions, for example, Fig. 3b. Comparison of TME + /Drug- and TME + /Drug+ identified proteins with higher abundance upon drug treatment using RUBICON, for example, Fig. 3c. Among these proteins, the TME labeled ones were proteins that became more disordered in stressed conditions. They were identified as the intersections of significant hits in Fig. 3b and c, for example, and labeled with their gene name. Created with BioRender.com. b, Western Blot results for validation of proteins enriched from untreated or tunicamycin treated cells with or without TME using the RUBICON workflow. c, The number of proteins (protein counts) detected in TME labeled/unlabeled, and tunicamycin treated/untreated cells, shown on the top of each bar plot. Protein counts in each condition were calculated as the number of proteins detected in all triplicates. For this calculation, mass spectra were searched using MaxQuant without ‘Match between runs’. d, TME binders in Fig. 3a and b were enriched in intracellular proteins (for example, nucleus, cytoplasm, ER). On top of each bar shows the fold enrichment, followed by the significance level. P value was calculated by Fisher’s Exact Test; ‘ns’, no significance; *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. e, Enrichment analysis of TME binders in Fig. 3b. “Tunicamycin binders” refer to TME binders in tunicamycin treated condition. P value was calculated by Fisher’s Exact Test, and further adjusted by Benjamini-Hochberg procedure as the multi-test adjustment method. f, Protein-protein interaction network of the six proteins that became more disordered upon tunicamycin treatment. Green nodes denote the first neighbor of these proteins.
