ReviewMetabolomics : Official journal of the Metabolomic Society2024
Navigating common pitfalls in metabolite identification and metabolomics bioinformatics.
Review in Metabolomics : Official journal of the Metabolomic Society, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed.
- Bridging bench and bedside: translational omics ofEuropean respiratory review : an official journal of the European Respiratory Society · 2026Review
- Harnessing Probiotic LAB and Bacteriocins for Clean-Label Food Processing and Biopreservation: Omics, Molecular Innovations and Industrial Applications.Probiotics and antimicrobial proteins · 2026Review
- Untargeted Blubber Metabolomics Reveals Biochemical Signatures Associated with Physiological Status in Live, Free-Ranging Bottlenose Dolphins.Metabolites · 2026Article
- Large-scale discovery and annotation of substructure patterns in mass spectrometry profiles.Nature communications · 2026Article
- Pseudoenhanced Peak Efficiency in Liquid Chromatography-High Resolution Mass Spectrometry Using Multiple Second Derivatives.Journal of the American Society for Mass Spectrometry · 2026Article
- Leveraging 13C-Labeling to Assign Molecular Formulas to Unknown Yeast Metabolites.Journal of the American Society for Mass Spectrometry · 2026Article
- IMFrag: A Tool to Recognize In-Source Fragmentation in Ion Mobility-Enabled Data-Independent Acquisition Workflows.Analytical chemistry · 2026Article
- Steroid Fingerprinting with Cryogenic Gas-Phase Infrared Spectroscopy.ACS measurement science au · 2026Article
- Untargeted metabolomics suggests a trade-off between phenolamides and flavonoids in the pollen of Petunia hybrida with contrasting flower colours.BMC plant biology · 2026Article
- PMconv: How to Compare Proteomes and Metabolomes?International journal of molecular sciences · 2026Article
- Emerging Quantitative Targeted Metabolomics Approaches for Future Inborn Errors of Metabolism Screening.Diagnostics (Basel, Switzerland) · 2026Review
- Lipid Class Prediction from MS1 Data using Gaussian Graphical Models.Analytical chemistry · 2026Article
- Identification of novel sugar-small-molecule conjugates in human urine based on multi-energy LC-MS/MS analysis.Analytical and bioanalytical chemistry · 2026Article
- Assessing current capabilities for incorporating lipidomics in multiomics data integration.Briefings in bioinformatics · 2026Review
- ILDMDB: a manually curated database of metabolite-disease associations in interstitial lung diseases.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Evaluation of MassFrontier, MetFrag, MS-FINDER, and SIRIUS for Metabolite Annotation Using an Experimental LC-HRMS Dataset.Biomedicines · 2026Article
- Mapping the unknown: an anchor-based molecular networking workflow for comprehensive identification of new psychoactive substances and analogues.Analytical and bioanalytical chemistry · 2026Article
- Large-Scale Metabolite Annotation in Untargeted Metabolomics Using MetDNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Pilot longitudinal integrated transcriptomic-metabolomic study reveals immune and metabolic signatures in non-hospitalized healthcare workers with long COVID.Frontiers in cellular and infection microbiology · 2026Article
- MetScribeR: A Semiautomated Tool for Data Processing of In-House LC-MS Metabolite Reference Libraries.Journal of proteome research · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetabolomics, the systematic analysis of small molecules in a given biological system, emerged as a powerful tool for different research questions. Newer, better, and faster methods have increased the coverage of metabolites that can be detected and identified in a shorter amount of time, generating highly dense datasets. While technology for metabolomics is still advancing, another rapidly growing field is metabolomics data analysis including metabolite identification. Within the next years, there will be a high demand for bioinformaticians and data scientists capable of analyzing metabolomics data as well as chemists capable of using in-silico tools for metabolite identification. However, metabolomics is often not included in bioinformatics curricula, nor does analytical chemistry address the challenges associated with advanced in-silico tools. AIM OF REVIEW: In this educational review, we briefly summarize some key concepts and pitfalls we have encountered in a collaboration between a bioinformatician (originally not trained for metabolomics) and an analytical chemist. We identified that many misunderstandings arise from differences in knowledge about metabolite annotation and identification, and the proper use of bioinformatics approaches for these tasks. We hope that this article helps other bioinformaticians (as well as other scientists) entering the field of metabolomics bioinformatics, especially for metabolite identification, to quickly learn the necessary concepts for a successful collaboration with analytical chemists. KEY SCIENTIFIC CONCEPTS OF REVIEW: We summarize important concepts related to LC-MS/MS based non-targeted metabolomics and compare them with other data types bioinformaticians are potentially familiar with. Drawing these parallels will help foster the learning of key aspects of metabolomics.
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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.