Updated project metadata. A large-scale discovery proteomics experiment was performed on biomass of Nitrospira moscoviensis (Lab head, Dr. Sebastian Lücker, RU, NL). The soluble protein fraction was analysed following high pH reverse-phase peptide fractionation. The insoluble membrane fraction was solubilised by an optimised protocol and analysed following cleavage using different proteolytic enzymes to maximise proteome coverage.