Fig. 4: DIA-DOMs reveal the cellular effects of starvation and Bafilomycin A1 treatment.

HeLa cells were either left untreated, or starved in the presence of 100 nM BafA for 1 h. DIA-DOMs were prepared in triplicate. a PCA maps show overall similar topology in both conditions. Source data are provided as a Source Data file. b Movement-Reproducibility (M-R) analysis detects 164 proteins with significantly altered subcellular localization (marked in red and black) at an FDR < 5%, which corresponds to an M-score cut-off at 1.3. The M-score is the −log10 of the Benjamini-Hochberg corrected combination of p-values derived from three independent chi2 distributions of robust Mahalanobis distances (see Methods for details). In addition, the R-score cut-off was 0.75, and proteins with only one replicate p-value < 0.1 were excluded. Integral Golgi membrane proteins with significant M-R scores are marked in black. c Hierarchical clustering of the 164 significant profile shifts by Pearson correlation. Cluster annotation is based on GO-term annotation enrichment (see Supplementary Fig. 4C); the brown clusters show no significant enrichments at 10% FDR. As expected, we did not observe the re-localization of core autophagic machinery, since HeLa cells already have high basal levels of autophagy (see Supplementary Fig. 6C). d Profiles of three significantly shifting Golgi proteins, overlayed with average profiles for Golgi markers (non-treated, nt) and endosome markers (starved/BafA treated, tr). GLG1 and TM9SF2 show complete transitions from Golgi to endosomes, and TM9SF4 only a partial transition.