MyCompoundID: using an evidence-based metabolome library for metabolite identification
Abstract
Identification of unknown metabolites is a major challenge in metabolomics. Without the identities of the metabolites, the metabolome data generated from a biological sample cannot be readily linked with the proteomic and genomic information for studies in systems biology and medicine. We have developed a web-based metabolite identification tool ( http://www.mycompoundid.org ) that allows searching and interpreting mass spectrometry (MS) data against a newly constructed metabolome library composed of 8,021 known human endogenous metabolites and their predicted metabolic products (375,809 compounds from one metabolic reaction and 10,583,901 from two reactions). As an example, in the analysis of a simple extract of human urine or plasma and the whole human urine by liquid chromatography-mass spectrometry and MS/MS, we are able to identify at least two times more metabolites in these samples than by using a standard human metabolome library. In addition, it is shown that the evidence-based metabolome library (EML) provides a much superior performance in identifying putative metabolites from a human urine sample, compared to the use of the ChemPub and KEGG libraries.
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Software tools such as MetFrag, MyCompoundID, MetiTree, and Mass Frontier can handle metabolite fragmentation data and permit library searches for candidates using in silico fragmentation predictions or comparisons to previously fragmented metabolites or standards.
“Software tools such as MetFrag, MyCompoundID, MetiTree, and Mass Frontier can handle metabolite fragmentation data and permit library searches for potential candidates using in silico fragmentation predictions of metabolites or comparisons to previously fragmented metabolites or standards (146, 153-155).”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [146]
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- Authors
- Li, L., Li, R., Zhou, J., Zuniga, A., Stanislaus, A. E., Wu, Y., Huan, T., Zheng, J., Shi, Y., Wishart, D. S., & Lin, G.
- Affiliations
- University of Alberta (CA)
- Corresponding author
- Li, Liang
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2013-03-06
- Volume
- 85
- Issue
- 6
- Pages
- 3401-3408
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2077488126
- Cited by
- 229
- References
- 24
- Citations by year
- 2026: 14 · 2025: 13 · 2024: 22 · 2023: 20 · 2022: 14 · 2021: 16 · 2020: 24 · 2019: 18 · 2018: 18 · 2017: 20 · 2016: 16 · 2015: 11 · 2014: 17 · 2013: 6
- FWCI
- 7.47
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- metabolite identification, mass spectral interpretation, human urine, plasma, liquid chromatography-mass spectrometry, tandem mass spectrometry
- MeSH terms
- Chromatography, Liquid, Humans, Databases, Factual, Libraries, Digital, Tandem Mass Spectrometry, Metabolic Networks and Pathways, Metabolome
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