Fig. 3

Peptide identification metrics in human and mouse gut metaproteomic data obtained using different databases. a Results obtained with human (N = 3, left) and mouse (N = 3, right) samples, with each dot representing a single sample. R-A and C-A are referred to DBs constructed with metagenomic reads and contigs from all samples, respectively. UP-B indicates a UniProt-based DB containing all bacterial entries. Ampersand indicates merging results from parallel DB searches. Asterisks indicate significantly different peptide identification yields between DBs (*p < 0.05; **p < 0.01; ***p < 0.001; paired t test), with the asterisk color corresponding to the DB to which the comparison is referred (e.g., the green asterisk over blue dots indicates significance of the difference between “R-A” and “R-A & UP-B”). b Comparison of metagenomic DB construction strategies applied to human (N = 3, left) and mouse (N = 3, right) samples, with each dot representing a single sample. “R” and “C” refer to reads (blue) and contigs (red), respectively. Matched DBs (sequences from the gut metagenome of the same subject analyzed by metaproteomics) are indicated with “-M,” unmatched DBs (sequences from a gut metagenome of another subject of the same host species) are indicated with “-UM;” merged DBs (sequences from gut metagenomes of all subjects analyzed for that host species) are indicated with “-A.” *p < 0.05 (paired t test)