This is a re-analysis of the saliva metaproteome dataset by Grassl et al. (Grassl et al. 2016 Genome Med, 8(1):44 DOI: 10.1186/s13073-016-0293-0) available on ProteomeXchange PXD003028. The data was used as a case study for a method development study in which we developed metaproteomics based methods for quantifying taxonomic composition of microbiomes (microbial communities). We used the fraction data from the original study for individuals 1 (female1), 3 (female3), 5 (male1), and 7 (male3).