Data used in "Fast metabolite identification with Input Output Kernel Regression"

  • Céline Brouard (Contributor)
  • Huibin Shen (Contributor)
  • Kai Dührkop (Contributor)
  • Florence d'Alché-Buc (Université Paris-Saclay) (Creator)
  • Sebastian Böcker (Creator)
  • Juho Rousu (Contributor)

Dataset

Description

This repository contains the data used in [1] to evaluate the performance for metabolite identification from tandem mass spectra. These data have been extracted and processed in [2]. We used a subset of 4138 MS/MS spectra extracted from the GNPS public spectral library (https://gnps.ucsd.edu/ProteoSAFe/libraries.jsp) for training and evaluation. For searching, we used molecular structures from PubChem as candidate sets.


Please mention and cite GNPS when using these data.


The implementation of the method proposed in [1] is available on: https://version.aalto.fi/gitlab/kepaco/Fast-metabolite-identification-with-IOKR


Files description:




spectra.txt: informations about the MS/MS spectra (GNPS identifier, compound name and INCHI identifier)

data_GNPS.mat: contains the molecular fingerprints, molecular formula and InCHI corresponding to the MS/MS spectra

cv_ind.txt: indices of the cross-validation folds

ind_eval.txt: indices of the examples used for evaluation

candidates: fingerprints and INCHI for the different candidate sets

input_kernels: contains 24 input kernel matrices


References:


[1] Brouard, C., Shen, H., Dührkop, K., d'Alché-Buc, F., Böcker, S. and Rousu, J.: Fast metabolite identification with Input Output Kernel Regression. In the proceedings of ISMB 2016, Bioinformatics 32(12): i28-i36, 2016. DOI: https://doi.org/10.1093/bioinformatics/btw246


[2] Dührkop, K., Shen, H., Meusel, M., Rousu, J. and Böcker, S.: Searching molecular structure databases with tandem mass spectra using CSI:FingerID. PNAS, 112(41), 12580-12585, 2015. doi:10.1073/pnas.1509788112


 


 
Date made available29 Jun 2017

Dataset Licences

  • CC-BY-4.0

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