ArticleFrontiers in bioengineering and biotechnology2014
MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments.
Article in Frontiers in bioengineering and biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.Metabolomics : Official journal of the Metabolomic Society · 2023Pooled it
- A Metabolome Atlas of Grape Biodiversity.Journal of agricultural and food chemistry · 2026Article
- Metabolomics meets systems immunology.EMBO reports · 2023Review
- A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research.Metabolites · 2022Review
- Optimization of metabolomic data processing using NOREVA.Nature protocols · 2022Review
- Grapevine and Wine Metabolomics-Based Guidelines for FAIR Data and Metadata Management.Metabolites · 2021Article
- Use of Untargeted Liquid Chromatography-Mass Spectrometry Metabolome To Discriminate Italian Monovarietal Red Wines, Produced in Their Different Terroirs.Journal of agricultural and food chemistry · 2020Article
- NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data.Nucleic acids research · 2020Article
- Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops.The Plant journal : for cell and molecular biology · 2020Article
- LC-MS untargeted approach showed that methyl jasmonate application on Vitis labrusca L. grapes increases phenolics at subtropical Brazilian regions.Metabolomics : Official journal of the Metabolomic Society · 2020Article
- The metaRbolomics Toolbox in Bioconductor and beyond.Metabolites · 2019Review
- NOREVA: normalization and evaluation of MS-based metabolomics data.Nucleic acids research · 2017Article
- From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics.GigaScience · 2017Review
- Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis.Scientific reports · 2016Article
- The WEIZMASS spectral library for high-confidence metabolite identification.Nature communications · 2016Article
- Data standards can boost metabolomics research, and if there is a will, there is a way.Metabolomics : Official journal of the Metabolomic Society · 2016Review
- Improved batch correction in untargeted MS-based metabolomics.Metabolomics : Official journal of the Metabolomic SocietyArticle
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata organization, quality assessment, data processing, data storage, and, finally, submission to public repositories, bioinformatic pipelines of a non-interactive nature are often employed, complementing the interactive software used for initial inspection and visualization of the data. These pipelines often are created as open-source software allowing the complete and exhaustive documentation of each step, ensuring the reproducibility of the analysis of extensive and often expensive experiments. In this paper, we will review the major steps which constitute such a data processing pipeline, discussing them in the context of an open-source software for untargeted MS-based metabolomics experiments recently developed at our institute. The software has been developed by integrating our metaMS R package with a user-friendly web-based application written in Grails. MetaMS takes care of data pre-processing and annotation, while the interface deals with the creation of the sample lists, the organization of the data storage, and the generation of survey plots for quality assessment. Experimental and biological metadata are stored in the ISA-Tab format making the proposed pipeline fully integrated with the Metabolights framework.
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Registered trials
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.