ArticleAnalytical chemistry2023
Generalized Tree Structure to Annotate Untargeted Metabolomics and Stable Isotope Tracing Data.
Article in Analytical chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
12 citing papers in PubMed.
- Using MetaboAnalyst 6.0 for exposomics data analysis-from LC-MS2 spectra processing to dose-response modeling and causal inference.Nature protocols · 2026Review
- Assessing the metabolomics "dark matter" by a detectable khipu model.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- The neuro-skeletal crosstalk: Mechanisms, clinical implications, and smart material interventions.Journal of orthopaedic translation · 2026Review
- Metabolomics Data Processing Using the Asari Toolkit.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Practicing Data Science in Interactive Notebooks.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Review
- Constructing a consensus serum metabolome.bioRxiv : the preprint server for biology · 2025Article
- Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web.Journal of the American Society for Mass Spectrometry · 2024Article
- Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline.PLoS computational biology · 2024Article
- MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics.Nature communications · 2024Article
- Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline.bioRxiv : the preprint server for biology · 2024Article
- Trackable and scalable LC-MS metabolomics data processing using asari.Nature communications · 2023Article
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2 authors.
Funding
Abstract
In untargeted metabolomics, multiple ions are often measured for each original metabolite, including isotopic forms and in-source modifications, such as adducts and fragments. Without prior knowledge of the chemical identity or formula, computational organization and interpretation of these ions is challenging, which is the deficit of previous software tools that perform the task using network algorithms. We propose here a generalized tree structure to annotate ions in relationships to the original compound and infer neutral mass. An algorithm is presented to convert mass distance networks to this tree structure with high fidelity. This method is useful for both regular untargeted metabolomics and stable isotope tracing experiments. It is implemented as a Python package (khipu) and provides a JSON format for easy data exchange and software interoperability. By generalized preannotation, khipu makes it feasible to connect metabolomics data with common data science tools and supports flexible experimental designs.
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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.