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.