(i) Database searching

Tandem mass spectra were extracted by Proteome Discoverer (Thermo-Fisher) version 2.2.0.388. Charge state deconvolution and deisotoping were not performed. All MS/MS samples analyzed were processed by a thorough database searching considering biological modification and amino acid substitution against a non-redundant Uniprot E. coli strain K12 database (4,448 entries), E. coli O157:H7 strain EDL933, UP000028484 (5,270 entries) and E_coli_O157_20160822 database (75243 entries) with decoy option using MASCOT 2.4 (Matrix Science Inc., Boston, MA, USA) assuming the digestion enzyme trypsin. Mascot was searched with a fragment ion mass tolerance of 0.6–0.02 Da and a parental ion tolerance of 20–10 ppm. Methylthio of cysteine and iTRAQ8plex of lysine and the n-terminus were specified in Mascot as fixed modifications. Gln->pyro-Glu of the n-terminus, deamidated of asparagine and glutamine, methyl of lysine, oxidation of methionine, phospho of serine, threonine and tyrosine, nmethylmaleimide of cysteine and iTRAQ8plex of tyrosine were specified in Mascot as variable modifications.