Fig. 4: SHVIP complements and extends AP-MS data.

a Workflow for AP-MS experiments. Transgenic HSV-1 viruses individually expressing the indicated HA-tagged protein variants were used to infect HELFs (n = 3 biological replicates), followed by anti-HA enrichment and LC-MS measurement. Purifications were compared to control experiments with HSV-1 wildtype (WT) not expressing any HA-tagged bait. The intensity ratio comparing HA-bait to control enrichments was computed for individual co-enriched proteins (Volcano plots for all baits are included in Supplementary Fig. 3). b For comparing to AP-MS data, proteins in the SHVIP interactome (see also Fig. 2a) were categorized into proteins cross-linked to the bait (level 1), proteins cross-linked to the bait via one other protein (level 2), or higher-order interactors and proteins not contained in the structural interactome (>level 2/no interactors). c Log2 fold-changes in the respective AP-MS experiment comparing the protein categories from (b). Boxes represent lower and upper quartiles with median marked as horizontal line. Whiskers represent 1.5 times interquartile range. Outliers (points outside the whiskers) removed for visibility. P values are based on a two-sided Wilcoxon rank-sum test. Comparison of the interactome of the 8 selected viral proteins in SHVIP and AP-MS at a higher stringency (d) and lower stringency (e) log2 fold-change cut-off applied to AP-MS data. An additional t test P value cut-off (AP-MS P values, two-sided t tests without multiple hypothesis correction, n = 3 biological replicates) of 0.01 was applied to potential AP-MS interactors. The displayed P values indicate the statistical significance of the overlap between proteins identified via AP-MS and SHVIP and are based on one-sided Fisher’s Exact test. f Comparing the overlap between SHVIP and AP-MS and its statistical significance using a sliding AP-MS fold-change cut-off. P values are based on one-sided Fisher’s Exact test. g Representative depiction of SHVIP interactomes for selected proteins. Color coding of interacting nodes according to the co-enrichment ratios with the bait in AP-MS. h AP-MS co-enrichment levels of UL49 interactors found by SHVIP. Interactors are grouped into different biological categories. Source data are provided.