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UC2 search: using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics

SUMMARY: For metabolite annotation in metabolomics, variations in the registered states of compounds (charged molecules and multiple components, such as salts) and their redundancy among compound databases could be the cause of misannotations and hamper immediate recognition of the uniqueness of met...

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Detalles Bibliográficos
Autores principales: Sakurai, Nozomu, Narise, Takafumi, Sim, Joon-Soo, Lee, Chang-Muk, Ikeda, Chiaki, Akimoto, Nayumi, Kanaya, Shigehiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860614/
https://www.ncbi.nlm.nih.gov/pubmed/29040459
http://dx.doi.org/10.1093/bioinformatics/btx649
Descripción
Sumario:SUMMARY: For metabolite annotation in metabolomics, variations in the registered states of compounds (charged molecules and multiple components, such as salts) and their redundancy among compound databases could be the cause of misannotations and hamper immediate recognition of the uniqueness of metabolites while searching by mass values measured using mass spectrometry. We developed a search system named UC2 (Unique Connectivity of Uncharged Compounds), where compounds are tentatively neutralized into uncharged states and stored on the basis of their unique connectivity of atoms after removing their stereochemical information using the first block in the hash of the IUPAC International Chemical Identifier, by which false-positive hits are remarkably reduced, both charged and uncharged compounds are properly searched in a single query and records having a unique connectivity are compiled in a single search result. AVAILABILITY AND IMPLEMENTATION: The UC2 search tool is available free of charge as a REST web service (http://webs2.kazusa.or.jp/mfsearcher) and a Java-based GUI tool. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.