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Critical assessment of chromatographic metadata in publicly available metabolomics data repositories
INTRODUCTION: 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 identific...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Springer US
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9701651/ https://www.ncbi.nlm.nih.gov/pubmed/36436113 http://dx.doi.org/10.1007/s11306-022-01956-x |
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author | Harrieder, Eva-Maria Kretschmer, Fleming Dunn, Warwick Böcker, Sebastian Witting, Michael |
author_facet | Harrieder, Eva-Maria Kretschmer, Fleming Dunn, Warwick Böcker, Sebastian Witting, Michael |
author_sort | Harrieder, Eva-Maria |
collection | PubMed |
description | INTRODUCTION: 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. OBJECTIVES: 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. METHODS: 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. RESULTS: 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. CONCLUSION: Reporting of chromatographic metadata is currently not unified. Our recommended suggestions for metadata reporting will enable more standardization and automatization in future reporting. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11306-022-01956-x. |
format | Online Article Text |
id | pubmed-9701651 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Springer US |
record_format | MEDLINE/PubMed |
spelling | pubmed-97016512022-11-29 Critical assessment of chromatographic metadata in publicly available metabolomics data repositories Harrieder, Eva-Maria Kretschmer, Fleming Dunn, Warwick Böcker, Sebastian Witting, Michael Metabolomics Original Article INTRODUCTION: 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. OBJECTIVES: 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. METHODS: 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. RESULTS: 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. CONCLUSION: Reporting of chromatographic metadata is currently not unified. Our recommended suggestions for metadata reporting will enable more standardization and automatization in future reporting. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11306-022-01956-x. Springer US 2022-11-27 2022 /pmc/articles/PMC9701651/ /pubmed/36436113 http://dx.doi.org/10.1007/s11306-022-01956-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Original Article Harrieder, Eva-Maria Kretschmer, Fleming Dunn, Warwick Böcker, Sebastian Witting, Michael Critical assessment of chromatographic metadata in publicly available metabolomics data repositories |
title | Critical assessment of chromatographic metadata in publicly available metabolomics data repositories |
title_full | Critical assessment of chromatographic metadata in publicly available metabolomics data repositories |
title_fullStr | Critical assessment of chromatographic metadata in publicly available metabolomics data repositories |
title_full_unstemmed | Critical assessment of chromatographic metadata in publicly available metabolomics data repositories |
title_short | Critical assessment of chromatographic metadata in publicly available metabolomics data repositories |
title_sort | critical assessment of chromatographic metadata in publicly available metabolomics data repositories |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9701651/ https://www.ncbi.nlm.nih.gov/pubmed/36436113 http://dx.doi.org/10.1007/s11306-022-01956-x |
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