MetaMiner (former MetaRiPPquest) is a computational tool developed for peptidogenomic-based identification of post-translationally modified peptides (RiPPs) by combining genome/metagenome mining with analysis of tandem mass spectra.

You can try MetaMiner workflow online at GNPS website (registration is needed but it is quick and simple).

Also, we provide the command line version as part of the NPDtools package. Running instructions are specified in the README file (also available inside the package). The package is released under the Apache 2.0 License. The package includes sample mass spectra and genomic data for trying various MetaMiner running modes.

Download the latest NPDtools binaries (for 64-bit Linux or macOS)


In case of any questions, suggestions, bug reports, please write to .

The tool is developed in collaboration with University of California, San Diego and Carnegie Mellon University.


  1. Liu Cao, Alexey Gurevich , Kelsey L Alexander, C. Benjamin Naman, Tiago Leao, Evgenia Glukhov, Nathan A Moss, Tal Luzzatto Knaan, Fernando Vargas, Robby Quinn, Amina Bouslimani, Louis-Felix Nothias, Nitin K Singh, John G Sanders, Rodolfo A S Benitez, Luke R Thompson, Md-Nafiz Hamid, James T Morton, Alla Mikheenko , Alexander Shlemov ,  Anton Korobeynikov , Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William Gerwick, Lena Gerwick, Peter C. Dorrestein, Pavel A. Pevzner , Hosein Mohimani MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities Cell Systems, 2019