Fig. 2

Peptide identification metrics in human gut metaproteomic data obtained using different databases. a Non-redundant peptides identified by searching the MS spectra obtained from a human stool sample against 19 different types of sequence DBs. Each graph illustrates the results achieved using a different bioinformatic platform, namely (from left to right) MetaProteomeAnalyzer (MPA), MaxQuant (MQ), and Proteome Discoverer (PD). RF and R6 (in blue) represent sequence DBs based on metagenomic reads processed by FragGeneScan or six-frame translation, respectively, while CF and C6 (in red) represent sequence DBs based on metagenomic assembled contigs processed by FragGeneScan or six-frame translation, respectively; 18, 6, and 3 are referred to the sequencing depth (in gigabases). Data from UniProt-based DBs are depicted in green (“pseudo-metagenomes” based on taxa found by 16S rDNA gene analysis), orange (sequences selected based on taxa found by a proteomic iterative approach, PI; see Methods for further details), and turquoise (all bacterial sequences); F, G and S are referred to the level of taxonomic filtering (family, genus, and species, respectively). Each column in the histograms contains a darker (identifications with FDR <1 %) and a lighter part (additional identifications with FDR <5 %). b Total peptide identifications obtained using five representative DBs and related multiple DB searches (ampersand indicates merging results from different DBs). All searches were run in triplicate using the three abovementioned bioinformatic platforms