Database-independent de novo metaproteomics of complex microbial communities

Metaproteomics has emerged as one of the most promising approaches for determining the composition and metabolic functions of complete microbial communities. Conventional metaproteomics approaches rely on the construction of protein sequence databases and efficient peptide-spectrum-matching algorithms, an approach that is intrinsically biased towards the content of the constructed sequence database. Here, we introduce a highly efficient, database-independent de novo metaproteomics approach and systematically evaluate its quantitative performance using synthetic and natural microbial communities comprising dozens of taxonomic families. Our work demonstrates that the de novo sequencing approach can vastly expand many metaproteomics applications by enabling rapid quantitative profiling and by capturing unsequenced community members that otherwise remain inaccessible for further interpretation. Kleikamp et al., describe a novel de novo metaproteomics pipeline (NovoBridge) that enables rapid community profiling without the need for constructing protein sequence databases. [Display omitted] •NovoBridge—a novel de novo metaproteomics pipeline•Database-matching independent metaproteomic analysis of microbes•Rapid quantitative profiling of microbial communities•Novel validation strategy for taxonomic annotations of de novo sequences Metaproteomics has emerged as one of the most promising post-genomics approaches. Kleikamp et al., describe a novel de novo metaproteomics pipeline (NovoBridge) that enables rapid community profiling without the need for constructing protein sequence databases. The performance was systematically evaluated using pure reference strains, synthetic communities, and natural communities.