ISDB: In Silico DataBase (of Natural Products)

Background

The ISDB repository contains in silico fragmented spectra of natural products, generated using cfm-predict 4 (DOI: 10.1021/acs.analchem.1c01465).

The initial database preparation and its application for dereplication were first described in:
Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication (DOI: 10.1021/acs.analchem.5b04804).

Content

Previous versions of ISDB contained predicted spectra for compounds aggregated within the LOTUS Initiative (DOI: 10.7554/eLife.70780) and included only “merged” spectra.

This version expands beyond taxon-restricted compounds and includes:

• Individual in silico spectra predictions (~1 million)
• Substructure annotations
• Data for compounds from Wikidata and LOTUS

File Structure

.zip Files

Each .zip file contains:

• All original outputs from cfm-predict 4
• Substructure annotations

Wikidata vs LOTUS Files

• Wikidata files: Contain spectra for nearly all compounds found in Wikidata, obtained using this query: https://w.wiki/Cvdo.
• LOTUS files: Contain spectra only for compounds with a “found in taxon” (P703) statement, obtained using this query: https://w.wiki/D35x.

Energy Levels: energyAll vs energySum

• energyAll files: Include spectra for three individual energy levels plus a summed spectrum (4 spectra per polarity per compound).
• energySum files: Contain only the summed spectrum (1 spectrum per polarity per compound).

Related Resources

• Building scripts: https://github.com/mandelbrot-project/spectral_lib_builder
• Matching scripts: https://github.com/mandelbrot-project/spectral_lib_matcher