ArticleJournal of the American Society for Mass Spectrometry2011
Mass spectrometry-based quantification of pseudouridine in RNA.
Article in Journal of the American Society for Mass Spectrometry, 2011. 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 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
30 citing papers in PubMed.
- Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.Nature communications · 2026Article
- Advances in Quantitative Techniques for Mapping RNA Modifications.Life (Basel, Switzerland) · 2025Review
- Mechanistic insight into the pseudouridylation of RNA.RNA biology · 2025Review
- Review
- Recent advances in methylation modifications of microRNA.Genes & diseases · 2025Review
- Deciphering the pseudouridine nucleobase modification in human diseases: From molecular mechanisms to clinical perspectives.Clinical and translational medicine · 2025Review
- Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease.Molecular biotechnology · 2024Review
- Advancements in pseudouridine modifying enzyme and cancer.Frontiers in cell and developmental biology · 2024Review
- Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing.Nature communications · 2023Article
- Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Direct Immunodetection of Global A-to-I RNA Editing Activity with a Chemiluminescent Bioassay.Angewandte Chemie (International ed. in English) · 2021Article
- Review
- Pseudouridine as a novel biomarker in prostate cancer.Urologic oncology · 2021Review
- Regulation and Function of RNA Pseudouridylation in Human Cells.Annual review of genetics · 2020Review
- Characterization of UVA-Induced Alterations to Transfer RNA Sequences.Biomolecules · 2020Article
- Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases.The Analyst · 2020Article
- Absolute Quantification of RNA or DNA Using Acid Hydrolysis and Mass Spectrometry.Analytical chemistry · 2019Article
- Oligonucleotide analysis by hydrophilic interaction liquid chromatography-mass spectrometry in the absence of ion-pair reagents.Journal of chromatography. A · 2019Article
- Predictive value of pseudouridine in prostate cancer.American journal of clinical and experimental urology · 2019Article
- Chemical Labeling and Affinity Capture of Inosine-Containing RNAs Using Acrylamidofluorescein.Bioconjugate chemistry · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Direct detection of pseudouridine (ψ), an isomer of uridine, in RNA is challenging. The most popular method requires chemical derivatization using N-cyclohexyl-N'-β-(4-methylmorpholinum ethyl) carbodiimide p-tosylate (CMCT) followed by radiolabeled primer extension mediated by reverse transcriptase. More recently, mass spectrometry (MS)-based approaches for sequence placement of pseudouridine in RNA have been developed. Nearly all of these approaches, however, only yield qualitative information regarding the presence or absence of pseudouridine in a given RNA population. Here, we have extended a previously developed liquid chromatography tandem mass spectrometry (LC-MS/MS) method to enable both the qualitative and quantitative analysis of pseudouridine. Quantitative selected reaction monitoring (SRM) assays were developed using synthetic oligonucleotides, with or without pseudouridine, and the results yielded a linear relationship between the ion abundance of the pseudouridine-specific fragment ion and the amount of pseudouridine-containing oligonucleotide present in the original sample. Using this quantitative SRM assay, the extent of pseudouridine hypomodification in the conserved T-loop of tRNA isolated from two different Escherichia coli strains was established.
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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.