A database of In-Silico predicted MS/MS spectrum of Natural Products

Download .zip Download .tar.gz View on GitHub

Welcome to ISDB GitHub Page.

Here you will find the full In-Silico MS/MS DataBase (ISDB) described in the paper "Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication". This ISDB contains in-silico predicted MS/MS fragmentation spectra in positive ion mode for 170 602 Natural Products (NPs) from the UNPD (Universal Natural Products Database).

How to use the ISDB ?

Instructions for using this ISDB in a dereplication workflow are available as pdf here (updated on 06/2016): workflow


  • An SDF version of the UNPD-ISDB is downloadable here: UNPD-SDF
  • The GNPS (Global Natural Products Social molecular networking) platform is accessible here : GNPS
  • The Tremolo tool used for the spectral matching against the ISDB is included inside the ISDB zip file. It's documentation is available here : Tremolo
  • The UNPD is accessible here : UNPD
  • CFM-ID has been used to generate the in-silico spectra. CFM-ID is freely available here : CFM-ID

Data availability.

  • the original UNPD-ISDB spectral file (.mgf format) is available in the git repo and at the following Zenodo repository DOI
  • an updated ISDB spectral file (.mgf format) build using multiples sources of natural products structures agglomerated in the frame of the LOTUS Initiative is archived the following Zenodo repository DOI


Want to complement the existing ISDB (other compounds, negative mode, adducts ...) ? Improvements, suggestions ? Please contact us : pierre-marie.allard(at)

Creative Commons License
ISDB is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.