Fig. 5

A Bar plots of the numbers of protein groups identified from the 12 species of the synthetic microbial community, from the other species, and without taxonomic annotation information. The protein sequence database was generated from the mixed metagenome data of the synthetic microbial community and the fecal sample using the MD1, MD2, and MD3 pipelines with different annotation tools. The MS data were mixed from the synthetic microbial community and the fecal sample. A merged protein sequence database of the 12 species and the fecal sample was used as the reference. B Venn diagrams of species identified from the in silico mixed metaproteome dataset and the fecal metaproteome dataset. The protein sequence databases were generated from the mixed metagenome data of the synthetic microbial community and the fecal sample or from the fecal sample only using the MD3 pipeline with different annotation tools