ArticleNature communications2020
A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 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.
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
52 citing papers in PubMed, 93 citations in OpenAlex.
- From nucleotides to intact transcripts through oligonucleotides: Integrated chromatographic strategies for therapeutic mRNA characterization.Analytical and bioanalytical chemistry · 2026Review
- Quantitative RNA modification mapping by mass spectrometry with isobaric tags and nucleobase fragment analysis.Nature communications · 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
- A nanogram-sensitive workflow for oligonucleotide mass spectrometry using ion-pair-free nanoflow HILIC and RNase benchmarking.Nucleic acids research · 2026Article
- Anticodon loop remodeling and D-stem shape drive the specific recognition of ANN-decoding tRNAs for t6A modification.Nucleic acids research · 2026Article
- Integrating mass spectrometry with Nanopore direct RNA sequencing forbioRxiv : the preprint server for biology · 2026Article
- Pseudouridylation landscape across 42bioRxiv : the preprint server for biology · 2026Article
- Systematic screening of archaeal MazF homologs reveals Tth-MazF1, a versatile, sequence-specific ribonuclease from Thermococcus thioreducens.Nucleic acids research · 2026Article
- Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent mbioRxiv : the preprint server for biology · 2026Article
- Development of an immobilized system for RNA modification analysis.Molecular omics · 2026Article
- Methods for Investigating the Sperm Epigenome.Advances in experimental medicine and biology · 2026Review
- The Secret Life of NJournal of molecular biology · 2025Review
- Top-Down Characterization of Yeast tRNA by Gas-Phase Fractionation and Collisionally Activated Dissociation Informed by Electron Photodetachment Charge Reduction Mass Spectrometry.Analytical chemistry · 2025Article
- Effective data visualization strategies in untargeted metabolomics.Natural product reports · 2025Review
- Comprehensive nucleoside analysis of archaeal RNA modification profiles reveals an mCell reports · 2025Article
- Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function.RNA (New York, N.Y.) · 2025Review
- RNA modifications in the tumor microenvironment: insights into the cancer-immunity cycle and beyond.Experimental hematology & oncology · 2025Review
- Chemical reactivity of RNA and its modifications with hydrazine.Communications chemistry · 2025Article
- FAST MS: Software for the Automated Analysis of Top-Down Mass Spectra of Polymeric Molecules Including RNA, DNA, and Proteins.Journal of the American Society for Mass Spectrometry · 2025Article
- 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
Corrections and comments
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Authors and funding
8 authors at 6 institutions in 3 countries.
Funding
Abstract
The field of epitranscriptomics continues to reveal how post-transcriptional modification of RNA affects a wide variety of biological phenomena. A pivotal challenge in this area is the identification of modified RNA residues within their sequence contexts. Mass spectrometry (MS) offers a comprehensive solution by using analogous approaches to shotgun proteomics. However, software support for the analysis of RNA MS data is inadequate at present and does not allow high-throughput processing. Existing software solutions lack the raw performance and statistical grounding to efficiently handle the numerous modifications found on RNA. We present a free and open-source database search engine for RNA MS data, called NucleicAcidSearchEngine (NASE), that addresses these shortcomings. We demonstrate the capability of NASE to reliably identify a wide range of modified RNA sequences in four original datasets of varying complexity. In human tRNA, we characterize over 20 different modification types simultaneously and find many cases of incomplete modification.
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What OpenQuestion holds
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.