ArticleAnalytical chemistry2015
Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS.
Article in Analytical chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 47 citations in OpenAlex.
- A nanogram-sensitive workflow for oligonucleotide mass spectrometry using ion-pair-free nanoflow HILIC and RNase benchmarking.Nucleic acids research · 2026Article
- Direct sequencing of totalRNA (New York, N.Y.) · 2023Article
- Landscape of Post-Transcriptional tRNA Modifications in Streptomyces albidoflavus J1074 as Portrayed by Mass Spectrometry and Genomic Data Mining.Journal of bacteriology · 2023Article
- Review
- Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcriptRNA (New York, N.Y.) · 2022Article
- Survey and Validation of tRNA Modifications and Their Corresponding Genes inBiomolecules · 2020Article
- Identification of the 3-amino-3-carboxypropyl (acp) transferase enzyme responsible for acp3U formation at position 47 in Escherichia coli tRNAs.Nucleic acids research · 2020Article
- Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases.The Analyst · 2020Article
- Identification and Characterization of Genes Required for 5-Hydroxyuridine Synthesis in Bacillus subtilis and Escherichia coli tRNA.Journal of bacteriology · 2019Article
- RNA-modifying enzymes and their function in a chromatin context.Nature structural & molecular biology · 2019Review
- To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs.IUBMB life · 2019Review
- Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry.Biochimica et biophysica acta. Gene regulatory mechanisms · 2019Review
- Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis.Nature communications · 2018Article
- Improving RNA modification mapping sequence coverage by LC-MS through a nonspecific RNase U2-E49A mutant.Analytica chimica acta · 2018Article
- Monitoring the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification in eukaryotic tRNAs via the γ-toxin endonuclease.RNA (New York, N.Y.) · 2018Article
- MODOMICS: a database of RNA modification pathways. 2017 update.Nucleic acids research · 2018Article
- Detecting RNA modifications in the epitranscriptome: predict and validate.Nature reviews. Genetics · 2017Review
- Stable Isotope Labeling for Improved Comparative Analysis of RNA Digests by Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2017Article
- Mapping Post-Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry.Biomolecules · 2017Review
- Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation.Biomolecules · 2017Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
There has been a renewed appreciation for the dynamic nature of ribonucleic acid (RNA) modifications and for the impact of modified RNAs on organism health resulting in an increased emphasis on developing analytical methods capable of detecting modifications within specific RNA sequence contexts. Here we demonstrate that a DNA-based exclusion list enhances data dependent liquid chromatography tandem mass spectrometry (LC-MS/MS) detection of post-transcriptionally modified nucleosides within specific RNA sequences. This approach is possible because all post-transcriptional modifications of RNA, except pseudouridine, result in a mass increase in the canonical nucleoside undergoing chemical modification. Thus, DNA-based sequences reflect the state of the RNA prior to or in the absence of modification. The utility of this exclusion list strategy is demonstrated through the RNA modification mapping of total tRNAs from the bacteria Escherichia coli, Lactococcus lactis, and Streptomyces griseus. Creation of a DNA-based exclusion list is shown to consistently enhance the number of detected modified ribonuclease (RNase) digestion products by ∼20%. All modified RNase digestion products that were detected during standard data dependent acquisition (DDA) LC-MS/MS were also detected when the DNA-based exclusion list was used. Consequently, the increase in detected modified RNase digestion products is attributed to new experimental information only obtained when using the exclusion list. This exclusion list strategy should be broadly applicable to any class of RNA and improves the utility of mass spectrometry approaches for discovery-based analyses of RNA modifications, such as are required for studies of the epitranscriptome.
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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.