Updated project metadata. The oral cavity is home to one of the most diverse microbial community of the human body and a major entry portal for pathogens. Its homeostasis is maintained by saliva, which fulfills key functions including lubrication of food, predigesting and bacterial defense. Consequently, disruptions in saliva secretion contributes to conditions such as tooth decay and respiratory tract infections. Here we used recent improvements in mass spectrometry (MS)-based proteomics to develop a rapid workflow for mapping to map the saliva proteome quantitatively and at great depth. Microgram protein amounts retrieved from cotton swabs were processed in a single-run format, resulting in more than 3,700 quantified human proteins in 100 min measurements gradients. After separation into eight fractions, this increased to 5,500 human proteins. Remarkably, our measurements also quantified more than 2,000 microbial proteins and we find peptide evidence for more than 70 bacterial genera without any microbial culture. Co-analysis of the proteomics results with next generation sequencing data as well as MALDI Biotyper revealed strong agreement. The oral microbiome differs between individuals and changes drastically upon eating and tooth brushing. Rapid and robust shotgun technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid.