Updated project metadata. We profiled both fractions of the urinary proteome for 33 human subjects with varied pathologies such as urinary tract infection (UTI), urogenital injury and commensal bacteria colonization. Using a LC-MS/MS based metaproteomic approach, we identified 5,327 non-redundant human proteins, 2,638 and 4,379 of which were associated with soluble urine (SU) and urinary pellet (UP) fractions, respectively, and approximately 1,206 non-redundant protein orthology groups derived from pathogens and commensal organisms of the urogenital tract