Male house mice were housed under semi-natural conditions and their urinary proteins were quantified using MS1 and MS2 based label-free strategies. This dataset consists of 52 raw MS files, comprising 26 DIA (SWATH) and 26 IDA runs on a TripleTOF 5600. The composition of the dataset is described in the manuscript by Enk et al., titled: "Regulation of highly homologous Major Urinary Proteins in house mice quantified with label-free proteomic methods ", Molecular Biosystems, in review.