Published August 10, 2020 | Version v1
Dataset Open

Cleaned and pre-processed MS/MS datset (build from all positive ionmode spectra in GNPS) - zip file

Creators

  • 1. Netherlands eScience Center
  • 2. University of Glascow
  • 3. Wageningen University

Description

Large MS/MS dataset build from data that was obtained from GNPS (accessed on 2020-05-11): https://gnps-external.ucsd.edu/gnpslibrary/ALL_GNPS.json

The data was cleaned and pre-processed using notebooks provided here: https://github.com/iomega/spec2vec_gnps_data_analysis/tree/master/notebooks

  • 112,956 positive ionmode spectra
  • metadata was cleaned and corrected using matchms (https://github.com/matchms/matchms) and lookup routines using PubChem
  • 92,954 of the spectra have Smiles and InchiKey (13717 unique InchiKey in first 14 characters)

 

Was used for the main article on Spec2Vec --> https://doi.org/10.1371/journal.pcbi.1008724

Files

gnps_positive_ionmode_cleaned_by_matchms_and_lookups.zip

Files (336.6 MB)

Additional details

Related works

Is part of
Journal article: 10.1371/journal.pcbi.1008724 (DOI)