Updated project metadata. We analyzed total proteome of three methyltransferase gene knockouts strains of Escherichia coli: ΔrsmF (JW5301), ΔrlmC (JW2756), ΔrlmE (JW3146) from Keio collection and wild type (WT). Proteins were assessed using IDA approach (i.e. Information Dependent Acquisition) and SWATH (Data-Independent Acquisition) on Sciex TripleTof 5600+ mass‐spectrometer with a NanoSpray III ion source (ABSciex, Canada) coupled to a NanoLC Ultra 2D+ nano‐HPLC system (Eksigent). Dataset covers 16 samples.