MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

Cell Syst. 2019 Dec 18;9(6):600-608.e4. doi: 10.1016/j.cels.2019.09.004. Epub 2019 Oct 16.


Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.

Keywords: computational mass spectrometry; metagenomics; microbial metabolites; natural products discovery; ribosomally synthesized and post-translationally modified peptides.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / methods*
  • Genomics / methods
  • Humans
  • Microbiota / genetics*
  • Peptides / chemistry
  • Protein Processing, Post-Translational / genetics*
  • Ribosomes / genetics
  • Software


  • Peptides