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Protein filtration and normalization steps. For 3584 proteins found in MaxQuant,38contaminants and missing values were removed in Perseus,39and proteins significantly enriched over background (no H2O2 control) were identified in a Significance A outliers test (FDR <0.05). The internal reference (LHR-APEX2 profile) was subtracted from all protein profiles, proteins were then normalized to the non-simulated (no LH) control, and ComBat batch corrected.40Maximum abundance values across all timepoints per replicate were subjected to a t test (Benjamini-Hochberg FDR <0.05) to identify significantly enriched proteins following LH treatment, resulting in 2439 proteins. See alsoFigures S2A–S2E and for the list of proteins and data tables refer toData S1.

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