Dereplicator is a computational tool developed for identification of known peptidic natural products (NRPs and RiPPs) from LC-MS/MS data. Given a database of chemical structures, Dereplicator generates in-silico mass spectra of compounds by predicting how they fragment during mass spectrometry, and compares them to experimental LC-MS/MS and detects similarities. The similarity score is converted to a statistical significance, and significant matches are reported. For identification of modified/mutated variants of known compounds please refer to VarQuest, for identification of nonpeptidic natural products (e.g., polyketides, lipids, terpenes, benzenoids, etc) please refer to Dereplicator+.

How to run

You can try Dereplicator workflow online at the GNPS website (registration is needed but it is quick and simple). See the documentation for details.


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 data and a chemical structure database.

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

Examples of output

Example of Dereplicator output on the whole publicly available GNPS data is here and its manual curation and evaluation are here.


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

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