Harrieder, Eva-Maria, Kretschmer, Fleming, Dunn, Warwick 
ORCID: 0000-0001-6924-0027, Boecker, Sebastian and Witting, Michael
(2022)
Critical assessment of chromatographic metadata in publicly available metabolomics data repositories.
METABOLOMICS, 18 (12).
97-.
Abstract
<h4>Introduction</h4>The 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.<h4>Objectives</h4>In 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.<h4>Methods</h4>We 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.<h4>Results</h4>We 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.<h4>Conclusion</h4>Reporting of chromatographic metadata is currently not unified. Our recommended suggestions for metadata reporting will enable more standardization and automatization in future reporting.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | Data reuse, LC-MS, Metabolomics, Repositories, Retention time |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 15 Dec 2023 11:01 |
| Last Modified: | 03 Feb 2024 10:00 |
| DOI: | 10.1007/s11306-022-01956-x |
| Open Access URL: | https://doi.org/10.1007/s11306-022-01956-x |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3177433 |
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