GNPS API Overview

GNPS Library Spectra

All Public Library Spectra at GNPS

https://gnps-external.ucsd.edu/gnpslibraryjson

All Public Library Specta at GNPS with Peaks and Annotation History

https://gnps-external.ucsd.edu/gnpslibraryformattedwithpeaksjson

Single Library Spectrum

https://gnps.ucsd.edu/ProteoSAFe/SpectrumCommentServlet?SpectrumID=<Library Accession>

Example

GNPS Jobs

Job Results API

GNPS job results page in JSON format:

https://gnps.ucsd.edu/ProteoSAFe/result_json.jsp?task=<task id>&view=<view name>

Example

Structure Conversion

Conversion to Smiles

https://gnps-structure.ucsd.edu/smiles?inchi=<inchi string>

Example

Conversion to InChI

https://gnps-structure.ucsd.edu/inchi?smiles=<smiles string>

Example

Conversion to InChIKey

https://gnps-structure.ucsd.edu/inchikey?smiles=<smiles string>

Example

Conversion to monoisotopic mass

https://gnps-structure.ucsd.edu/structuremass?smiles=<smiles string>

Example

Conversion to formula

https://gnps-structure.ucsd.edu/formula?smiles=<smiles string>

Example

Structure Classyfire

If you have Smiles or InChI

https://gnps-structure.ucsd.edu/classyfire?smiles=<smiles string>

Example

If you have InChI Key

https://gnps-classyfire.ucsd.edu/entities/<InChI Key>.json

Example

Structure Image

https://gnps-structure.ucsd.edu/structureimg?smiles=<smiles string>

Example

ReDU

Per File Sample Information Query

https://redu.ucsd.edu/filename?query=<File full path in MassIVE>

Example

GNPS Continuous ID Data

If you want to download all public datasets that have been processed by GNPS. You can find the dumps here:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=25cc4f9135c6428aabe1f41a9e54c369&view=advanced_view

This includes:

  1. Clustered MGFs for each dataset
  2. Identifications for clustered spectra
  3. Mapping of clusters back to original files and scans
  4. Molecular Networks for each dataset