MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
27 06 2022
27 06 2022
Historique:
received:
23
08
2021
revised:
25
03
2022
accepted:
16
05
2022
pubmed:
21
5
2022
medline:
15
11
2022
entrez:
20
5
2022
Statut:
ppublish
Résumé
Although advances in untargeted metabolomics have made it possible to gather data on thousands of cellular metabolites in parallel, identification of novel metabolites from these datasets remains challenging. To address this need, Metabolic in silico Network Expansions (MINEs) were developed. A MINE is an expansion of known biochemistry which can be used as a list of potential structures for unannotated metabolomics peaks. Here, we present MINE 2.0, which utilizes a new set of biochemical transformation rules that covers 93% of MetaCyc reactions (compared to 25% in MINE 1.0). This results in a 17-fold increase in database size and a 40% increase in MINE database compounds matching unannotated peaks from an untargeted metabolomics dataset. MINE 2.0 is thus a significant improvement to this community resource. The MINE 2.0 website can be accessed at https://minedatabase.ci.northwestern.edu. The MINE 2.0 web API documentation can be accessed at https://mine-api.readthedocs.io/en/latest/. The data and code underlying this article are available in the MINE-2.0-Paper repository at https://github.com/tyo-nu/MINE-2.0-Paper. MINE 2.0 source code can be accessed at https://github.com/tyo-nu/MINE-Database (MINE construction), https://github.com/tyo-nu/MINE-Server (backend web API) and https://github.com/tyo-nu/MINE-app (web app). Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 35595247
pii: 6589885
doi: 10.1093/bioinformatics/btac331
pmc: PMC9237697
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
3484-3487Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM008449
Pays : United States
Organisme : National Science Foundation
ID : MCB-1614953
Organisme : U.S. Department of Energy
ID : DE-SC0018249
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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