The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics
Open accessAbstract
The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.
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Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., Fan, T. W.-M., Fiehn, O., Goodacre, R., Griffin, J. L., et al. (2007) · Metabolomics · doi:10.1007/s11306-007-0082-2 · Cited by 5,368
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Schymanski, E. L., Jeon, J., Gulde, R., Fenner, K., Ruff, M., Singer, H. P., & Hollender, J. (2014) · Environmental Science & Technology · doi:10.1021/es5002105 · Cited by 4,519
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
Kind, T., & Fiehn, O. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-105 · Cited by 1,201
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Ma, J., Sheridan, R. P., Liaw, A., Dahl, G. E., & Svetnik, V. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/ci500747n · Cited by 1,159
The BRENDA enzyme information system–From a database to an expert system
Schomburg, I., Jeske, L., Ulbrich, M., Placzek, S., Chang, A., & Schomburg, D. (2017) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2017.04.020 · Cited by 222
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A Cardiovascular Disease-Linked Gut Microbial Metabolite Acts via Adrenergic Receptors
Nemet, I., Saha, P. P., Gupta, N., Zhu, W., Romano, K. A., Skye, S. M., Cajka, T., Mohan, M. L., Li, L., Wu, Y., et al. (2020) · Cell · doi:10.1016/j.cell.2020.02.016 · Cited by 784
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Review: Metabolomics as a Prediction Tool for Plants Performance under Environmental Stress
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Metadata
- Authors
- Blaženović, I., Kind, T., Ji, J., & Fiehn, O.
- Venue
- Metabolites
- Publisher
- MDPI AG
- Published
- 2018-05-10
- Volume
- 8
- Issue
- 2
- Pages
- 31
- ISSN
- 2218-1989 (ISSN-L)
- OpenAlex
- W2802909948
- Cited by
- 757
- References
- 6
- FWCI
- 20.56
- Type
- journal article
- Language
- en
- Open access
- gold
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