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. 2018 Feb 15;34(4):698-700.
doi: 10.1093/bioinformatics/btx649.

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

Nozomu Sakurai  1 , Takafumi Narise  1 , Joon-Soo Sim  2 , Chang-Muk Lee  2 , Chiaki Ikeda  1 , Nayumi Akimoto  1 , Shigehiko Kanaya  3 , Oliver Stegle
Affiliations

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

Nozomu Sakurai et al. Bioinformatics. .

Abstract

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.

Contact: sakurai@kazusa.or.jp.

Supplementary information: Supplementary data are available at Bioinformatics online.

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References

    1. Afendi F.M. et al. (2012) KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol., 53, e1. - PubMed
    1. Fahy E. et al. (2009) Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res., 50 (Suppl), S9–14. - PMC - PubMed
    1. Gu J. et al. (2013) Use of natural products as chemical library for drug discovery and network pharmacology. PLoS One, 8, e62839.. - PMC - PubMed
    1. Heller S. et al. (2013) InChI—the worldwide chemical structure identifier standard. J. Cheminform., 5, 1–9. - PMC - PubMed
    1. Iijima Y. et al. (2008) Metabolite annotations based on the integration of mass spectral information. Plant J., 54, 949–962. - PMC - PubMed

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