ArticleJournal of proteome research2018
Target-Decoy-Based False Discovery Rate Estimation for Large-Scale Metabolite Identification.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
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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
30 citing papers in PubMed.
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- The effects of combined low-dose cadmium and deltamethrin on mitochondrial bioenergetics and metabolism in human lung fibroblasts.Toxicology reports · 2025Article
- Vanadyl sulfate supplementation alters the intestinal microbiome and bile acid metabolism.Toxicology and applied pharmacology · 2025Article
- Extracellular Vesicles From Chylomicron-Treated Endothelial Cells Drive Macrophage Inflammation.Arteriosclerosis, thrombosis, and vascular biology · 2025Article
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- Sex Modifies Metabolic Pathways Associated with Lipids in Untargeted Metabolomics: The Coronary Artery Risk Development in Young Adults (CARDIA) Study, 2005-2006.Metabolites · 2025Article
- Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in post-transcriptional repression of starvation-induced pathways.bioRxiv : the preprint server for biology · 2025Article
- Cadmium exposure following early-life respiratory syncytial virus infection promotes lung fibrosis through autophagy inhibition.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Exploratory untargeted metabolomics analysis reveals differences in metabolite profiles in pregnant people exposed vs. unexposed to E-cigarettes secondhand in the NYU children's health and environment study.Metabolomics : Official journal of the Metabolomic Society · 2025Article
- The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency.Microbiome · 2025Article
- CYP3A5 unexpectedly regulates glucose metabolism through the AKT-TXNIP-GLUT1 axis in pancreatic cancer.Genes & diseases · 2024Article
- An assessment of AcquireX and Compound Discoverer software 3.3 for non-targeted metabolomics.Scientific reports · 2024Article
- Data Processing of Product Ion Spectra: Methods to Control False Discovery Rate in Compound Search Results for Untargeted Metabolomics.Mass spectrometry (Tokyo, Japan) · 2024Article
- PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements.Nature communications · 2023Article
- Article
- Effects of topping and non-topping on growth-regulating hormones of flue-cured tobacco (Frontiers in plant science · 2023Article
- Compound Identification Strategies in Mass Spectrometry-Based Metabolomics and Pharmacometabolomics.Handbook of experimental pharmacology · 2023Article
- The critical role that spectral libraries play in capturing the metabolomics community knowledge.Metabolomics : Official journal of the Metabolomic Society · 2022Review
- Low-Dose Cadmium Potentiates Metabolic Reprogramming Following Early-Life Respiratory Syncytial Virus Infection.Toxicological sciences : an official journal of the Society of Toxicology · 2022Article
- Mass spectrometry-based metabolomics in microbiome investigations.Nature reviews. Microbiology · 2022Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Metabolite identification is a crucial step in mass spectrometry (MS)-based metabolomics. However, it is still challenging to assess the confidence of assigned metabolites. We report a novel method for estimating the false discovery rate (FDR) of metabolite assignment with a target-decoy strategy, in which the decoys are generated through violating the octet rule of chemistry by adding small odd numbers of hydrogen atoms. The target-decoy strategy was integrated into JUMPm, an automated metabolite identification pipeline for large-scale MS analysis and was also evaluated with two other metabolomics tools, mzMatch and MZmine 2. The reliability of FDR calculation was examined by false data sets, which were simulated by altering MS1 or MS2 spectra. Finally, we used the JUMPm pipeline coupled to the target-decoy strategy to process unlabeled and stable-isotope-labeled metabolomic data sets. The results demonstrate that the target-decoy strategy is a simple and effective method for evaluating the confidence of high-throughput metabolite identification.
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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.