Database-independent de novo metaproteomics of complex microbial communities

Hugo B.C. Kleikamp, Mario Pronk, Claudia Tugui, Leonor Guedes da Silva, Ben Abbas, Yue Mei Lin, Mark C.M. van Loosdrecht, Martin Pabst*

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

19 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)375-383.e5
JournalCell Systems
Issue number5
Publication statusPublished - 2021


  • de novo peptide sequencing
  • metaproteomics
  • microbial communities


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