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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 — a tool for identification of peptidic natural products (PNPs) through database search of mass spectra
  • VarQuest — a tool for modification-tolerant identification of novel variants of PNPs
  • Dereplicator+ — a tool for identification of metabolites (both peptidic and non-peptidic) through database search of mass spectra
  • MetaMiner (former RiPPquest, MetaRiPPquest) — a tool implementing metabologenomics approach for the discovery of ribosomally synthesized and post-translationally modified peptides (RiPPs)

NPDtools pipelines are available online on GNPS and also released on GitHub as command-line tools. The latest release is NPDtools version 2.3.0 (January 9, 2019). The latest version of the manual explaining the installation and running of command-line utilities is available online at