ArticleNucleic acids research2025
Toward standardized epitranscriptome analytics: an inter-laboratory comparison of mass spectrometric detection and quantification of modified ribonucleosides in human RNA.
Article in Nucleic acids research, 2025. 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.
- Conversations at the crossroads of the Human RNome Project: a collaborative reflection by the RNome Early Career Researchers.RNA biology · 2026Article
- Mechanistic Insights Into the Oxidative Reactivity of 2-Selenouridine in tRNA.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- From nucleotides to intact transcripts through oligonucleotides: Integrated chromatographic strategies for therapeutic mRNA characterization.Analytical and bioanalytical chemistry · 2026Review
- RNA Modifications as Molecular Regulators of Alveolar Epithelial Injury and Aberrant Repair in Pulmonary Fibrosis.Biomolecules · 2026Review
- Harmonized nucleoside mass spectrometry enables reproducible cross-platform RNA modification quantification.bioRxiv : the preprint server for biology · 2026Article
- Human 28S rRNA analysed by state-of-the-art oligonucleotide mass spectrometry: benchmarking current capabilities and a call to action for MS-Seq.bioRxiv : the preprint server for biology · 2026Article
- Epitranscriptomic Analysis of A-to-I RNA Editing and mInternational journal of molecular sciences · 2026Review
- RNA-seq variants reveal distinct patterns in the aging epitranscriptome: an in-depth analysis of age-matched Alzheimer's Disease patients and a cognitively normal cohort.bioRxiv : the preprint server for biology · 2026Article
- GlycoRNA research: from unknown unknowns to known unknowns.Protein & cell · 2026Review
- RNA methylation in urological cancers: regulatory logic, biological functions, and clinical relevance.Frontiers in immunology · 2026Review
- Chalcogen-modified Nucleic Acid Analogues.Current medicinal chemistry · 2026Article
- Article
- Advances in Quantitative Techniques for Mapping RNA Modifications.Life (Basel, Switzerland) · 2025Review
- tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
The human RNome comprises all forms of RNA and the 50 + chemical structures-the epitranscriptome-that modify them. Understanding the diverse functions of RNA modifications in regulating gene expression and cell phenotype requires technologies such as RNA sequencing-based modification mapping and mass spectrometry-based quantification of modified ribonucleosides. Liquid chromatography-coupled tandem quadrupole mass spectrometry (LC-MS/MS) is the gold standard for detecting and quantifying modified ribonucleosides with accuracy and precision. However, variations in RNA isolation, processing, and LC-MS/MS analysis have hindered reproducibility across laboratories, which is essential for accurate quantification of RNA modifications. As guidance toward harmonization, we report a multi-laboratory comparison of workflows for LC-MS/MS RNA modification analysis. We compared protocols for sample shipment, RNA hydrolysis, LC-MS/MS analysis, and data processing among three laboratories working with the same total RNA samples. We detected and quantified 17 modifications consistently across protocols and operators, with another 7 that were sensitive to experimental conditions, reagent contamination, and ribonucleoside instability, leading to poor precision among laboratories. Agreement among the three labs was strong, with coefficients of variation of 20% and 10% for relative and absolute quantification, respectively. These findings establish a robust and readily adoptable epitranscriptome analytical platform that enables reliable comparisons across laboratories.
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