ArticleMethods (San Diego, Calif.)2016
Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry.
Article in Methods (San Diego, Calif.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 89 citations in OpenAlex.
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- RNase 4 improves bottom-up modification mapping ofbioRxiv : the preprint server for biology · 2026Article
- Pseudouridylation landscape across 42bioRxiv : the preprint server for biology · 2026Article
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- Unlocking the regulatory code of RNA: launching the Human RNome Project.Genome biology · 2025Article
- Toward standardized epitranscriptome analytics: an inter-laboratory comparison of mass spectrometric detection and quantification of modified ribonucleosides in human RNA.Nucleic acids research · 2025Article
- Key RNA-binding domains in the La protein establish tRNA modification levels in Trypanosoma brucei.Nucleic acids research · 2025Article
- Ion Mobility Gas-Phase Separation Enhances Top-Down Mass Spectrometry of Heavily Modified Guide RNA.Analytical chemistry · 2025Article
- The importance of physiological and disease contexts in capturing mRNA modifications.Nature structural & molecular biology · 2025Review
- Combining Nanopore direct RNA sequencing with genetics and mass spectrometry for analysis of T-loop base modifications across 42 yeast tRNA isoacceptors.Nucleic acids research · 2024Article
- Automated Identification of Modified Nucleosides during HRAM-LC-MS/MS using a Metabolomics ID Workflow with Neutral Loss Detection.Journal of the American Society for Mass Spectrometry · 2023Article
- Current technical advancements in plant epitranscriptomic studies.The plant genome · 2023Review
- mNature cell biology · 2023Article
- Direct sequencing of totalRNA (New York, N.Y.) · 2023Article
- A selective and sensitive detection system for 4-thiouridine modification in RNA.RNA (New York, N.Y.) · 2023Article
- mbioRxiv : the preprint server for biology · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Mass spectrometry is a powerful analytical tool for identifying and characterizing structural modifications to the four canonical bases in RNA, information that is lost when using techniques such as PCR for RNA analysis. Here we described an updated method for sequence mapping of modified nucleosides in transfer RNA. This modification mapping approach utilizes knowledge of the modified nucleosides present in the sample along with the genome-derived tRNA sequence to readily locate modifications site-specifically in the tRNA sequence. The experimental approach involves isolation of the tRNA of interest followed by separate enzymatic digestion to nucleosides and oligonucleotides. Both samples are analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) and the data sets are then combined to yield the modification profile of the tRNA. Data analysis is facilitated by the use of unmodified sequence exclusion lists and new developments in software that can automate MS/MS spectral annotation. The method is illustrated using tRNA-Asn isolated from Thermus thermophilus.
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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.