Dataset Open Access

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

Huber, Florian; Ridder, Lars; Verhoeven, Stefan; Spaaks, Jurriaan H.; Diblen, Faruk; Rogers, Simon; van der Hooft, Justin J.J.

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 (336.6 MB)
Name Size
gnps_positive_ionmode_cleaned_by_matchms_and_lookups.zip
md5:9c798b416a2e86bdb2ac562fe63b6972
336.6 MB Download
148
23
views
downloads
All versions This version
Views 148148
Downloads 2323
Data volume 7.7 GB7.7 GB
Unique views 125125
Unique downloads 1919

Share

Cite as