ArticleMethods in molecular biology (Clifton, N.J.)2019
Pre-analytic Considerations for Mass Spectrometry-Based Untargeted Metabolomics Data.
Article in Methods in molecular biology (Clifton, N.J.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Untargeted metabolomics reveals organism specific biomarkers of carbapenem resistance in Klebsiella pneumoniae and Escherichia coli.NPJ systems biology and applications · 2026Article
- Enhanced glycolysis and nicotinamide metabolism in HPV-positive head and neck cancer.Scientific reports · 2025Article
- Linear Dimensionality Reduction Methods for Analyzing Structured Biomedical Data: Existing Research and Future Opportunities.Wiley interdisciplinary reviews. Computational statistics · 2025Review
- Improved quantitative accuracy in data-independent acquisition proteomics via retention time boundary imputation.bioRxiv : the preprint server for biology · 2025Article
- Derangement in Nicotinamide Adenine Dinucleotide Metabolism is Observed During Acute Kidney Injury Among Male Agricultural Workers at Risk for Mesoamerican Nephropathy.Kidney international reports · 2024Article
- Transforming Big Data into AI-ready data for nutrition and obesity research.Obesity (Silver Spring, Md.) · 2024Review
- Proteomic analysis of the serum in dogs with pulmonary hypertension secondary to myxomatous mitral valve disease: the preliminary study.Frontiers in veterinary science · 2024Article
- Exploring the association of physical activity with the plasma and urine metabolome in adolescents and young adults.Nutrition & metabolism · 2023Article
- Article
- Advances in Microbial NMR Metabolomics.Advances in experimental medicine and biology · 2023Article
- A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research.Metabolites · 2022Review
- MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights.Nucleic acids research · 2021Article
- Tear Metabolomics in Dry Eye Disease: A Review.International journal of molecular sciences · 2019Review
- Predicting prognosis outcomes of primary central nervous system lymphoma with high-dose methotrexate-based chemotherapeutic treatment using lipidomics.Neuro-oncology advancesArticle
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Metabolomics is the science of characterizing and quantifying small molecule metabolites in biological systems. These metabolites give organisms their biochemical characteristics, providing a link between genotype, environment, and phenotype. With these opportunities also come data challenges, such as compound annotation, missing values, and batch effects. We present the steps of a general pipeline to process untargeted mass spectrometry data to alleviate the latter two challenges. We assume to have a matrix with metabolite abundances, with metabolites in rows and samples in columns. The steps in the pipeline include summarizing technical replicates (if available), filtering, imputing, transforming, and normalizing the data. In each of these steps, a method and parameters should be chosen based on assumptions one is willing to make, the question of interest, and diagnostic tools. Besides giving a general pipeline that can be adapted by the reader, our goal is to review diagnostic tools and criteria that are helpful when making decisions in each step of the pipeline and assessing the effectiveness of normalization and batch correction. We conclude by giving a list of useful packages and discuss some alternative approaches that might be more appropriate for the reader's data.
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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.