This dataset contains the mass spectrometry (LC–MS/MS) analysis of ZCWPW2-associated proteins in human testicular tissue. The study aimed to identify potential ZCWPW2-interacting partners. Protein complexes were immunoprecipitated using anti-ZCWPW2 antibodies and analyzed on a timsTOF Pro platform. The results provide a comprehensive proteomic profile of human testicular ZCWPW2 complexes.