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 NPDtools package, see links below. Running instructions are specified in the README file (also available inside the package). The package is released under the Apache 2.0 License.

Download NPDtools binaries for Linux (64-bit only)

Download NPDtools binaries for MacOS


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


Please cite the following if you are using MetaMiner (the paper is submitted):

Hosein Mohimani, Alexey Gurevich, Kelsey L Alexander, C Benjamin Naman, Tiago Leao, Evgenia Glukhov, Nathan A Moss, Tal Luzzatto Knaan, Fernando Vargas, Louis-Felix Nothias, Nitin K Singh, John G Sanders, Rodolfo AS 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
MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides
bioRxiv 227504; doi: