Fig. 4

Comparison of metaproteomic, shotgun metagenomic and 16S rRNA gene amplicon-based quantification of the mock communities. a The same mock communities as in Fig. 3 were used. For 16S rRNA gene amplicons and metaproteomes averages of four biological replicates per community type are shown. For the shotgun metagenomic data averages of three biological replicates are shown. For the metaproteomes the PSM-based quantification is shown (Fig. 3b). (gr − or gr + ) Gram-positive or -negative bacterium, (A) Archaeum, (E) Eukaryote, (V dsDNA, ssDNA or ssRNA) virus specifying nucleic acid type of genome. b–d Box plots show the x-fold deviation of the species abundance quantification with metaproteomics, metagenomics and 16S rRNA gene amplicon sequencing from the actual input amounts for protein (b) and (c), and cell number (d). c is an enlargement of the lower part of (b). If measured and input species abundance were equal, then all values would be exactly 0 (indicated by bright blue line). Zeros (species that were not detected i.e., ‘ND’ in a) were removed before plotting. For each community type and method the method with the significantly lowest x-fold deviation (p-value < 0.01, t test) is indicated with a bright blue ‘*’ (see Supplementary Table 4 for details on statistics). NA species not added to this mock community, ND not detected with this method