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

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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


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.