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NPDtools – Natural Product Discovery tools – is a toolkit containing various pipelines for in silico analysis of natural product mass spectrometry data.

The current version of NPDtools includes

  • Dereplicator — identification of peptidic natural products (PNPs) through database search of mass spectra
  • VarQuest — modification-tolerant identification of novel variants of PNPs
  • Dereplicator+ — identification of metabolites (both peptidic and non-peptidic) through database search of mass spectra
  • MetaMiner (former RiPPquest, MetaRiPPquest) — metabologenomics approach for the discovery of ribosomally synthesized and post-translationally modified peptides (RiPPs)
  • NPS approach for scoring and evaluating the statistical significance of peptidic natural product–spectrum matches (a part of Dereplicator and VarQuest)

NPDtools pipelines are available online on GNPS and also released on GitHub as command-line tools. The latest version of the manual explaining the installation and running of command-line utilities is available online.

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

We also co-authored several related Natural Product Discovery projects primarily developed at Mohimani Lab (Carnegie Mellon University) and/or Pevzner Lab (University of California, San Diego):


If you have any questions, suggestions, or bug reports, please write to or , or post an issue on GitHub.