List of 5,818 human proteins quantified with a minimum of three valid values in at least one setup of the dual proteome shotgun samples of S. Typhimurium infected human or control HeLa cells by means of data-independent acquisition (DIA).

Comparisons were analysed by t-testing and significant hits determined using as cut-off values a permutation based false discovery rate (FDR) of 0.01 and 0.001 (100 permutations) and a background variance parameter S0 of 0.1. (Regulated) host proteins previously found associated with Salmonella-modified membranes (SMM) [52] are indicated in indicated in columns ‘SMM proteome (PMID: 25348832)’ and/or ‘ANOVA regulated SMM protein’, respectively. Remaining table headers are as in S2 Table and cluster indication is as in S6 Fig. (XLSX)