Mass Spectrometry Experiment 1: Comparison of Mito Matrix and Vpu WT and mutants.

HeLa P4.R5 cells were transfected to express Mito (control) or Vpu constructs bearing C-terminal APEX2 tags, in duplicate. Following proximity biotinylation reactions, the biotinylated proteins were isolated and subject to quantitative mass spectrometry. Normalized TMT data are shown for duplicate samples. The mean normalized TMT data were sorted into 6 k-means clusters (presented as a heatmap in S3A Fig). Relative abundance of proteins was compared in Mito-APEX2 and Vpu(WT)-APEX2 samples, presented as log2 fold change Mito/Vpu. Significance for proteomics data was assessed by Student’s t-test, p values of p ≤ 0.05 were considered significant. Cellular component gene ontology (GO) analyses of proteins significantly enriched in Mito control vs Vpu WT are also shown. Enrichment scores are given as -Log10 p-values, the top five enriched cellular compartment GO-terms are presented in S3C Fig. (XLSX)