ArticleMetabolomics : Official journal of the Metabolomic Society2022
Critical assessment of chromatographic metadata in publicly available metabolomics data repositories.
Article in Metabolomics : Official journal of the Metabolomic Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Times are changing but order matters: transferable prediction of small-molecule liquid chromatography retention times.Nature methods · 2026Article
- Network-based integration of metabolomics data from large-scale repositories.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Integrating Sensory Evaluation and Metabolomics to Reveal the Metabolic Basis of Taste and Flesh Color in Melon (Metabolites · 2026Article
- ROASMI: accelerating small molecule identification by repurposing retention data.Journal of cheminformatics · 2025Article
- Mass spectrometry-based ginsenoside profiling: Recent applications, limitations, and perspectives.Journal of ginseng research · 2024Review
- Current Practices in LC-MS Untargeted Metabolomics: A Scoping Review on the Use of Pooled Quality Control Samples.Analytical chemistry · 2023Article
- The Expectation and Reality of the HepG2 Core Metabolic Profile.Metabolites · 2023Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
introductionThe structural identification of metabolites represents one of the current bottlenecks in non-targeted liquid chromatography-mass spectrometry (LC-MS) based metabolomics. The Metabolomics Standard Initiative has developed a multilevel system to report confidence in metabolite identification, which involves the use of MS, MS/MS and orthogonal data. Limitations due to similar or same fragmentation pattern (e.g. isomeric compounds) can be overcome by the additional orthogonal information of the retention time (RT), since it is a system property that is different for each chromatographic setup.
objectivesIn contrast to MS data, sharing of RT data is not as widespread. The quality of data and its (re-)useability depend very much on the quality of the metadata. We aimed to evaluate the coverage and quality of this metadata from public metabolomics repositories.
methodsWe acquired an overview on the current reporting of chromatographic separation conditions. For this purpose, we defined the following information as important details that have to be provided: column name and dimension, flow rate, temperature, composition of eluents and gradient.
resultsWe found that 70% of descriptions of the chromatographic setups are incomplete (according to our definition) and an additional 10% of the descriptions contained ambiguous and/or incorrect information. Accordingly, only about 20% of the descriptions allow further (re-)use of the data, e.g. for RT prediction. Therefore, we have started to develop a unified and standardized notation for chromatographic metadata with detailed and specific description of eluents, columns and gradients.
conclusionReporting of chromatographic metadata is currently not unified. Our recommended suggestions for metadata reporting will enable more standardization and automatization in future reporting.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.