ArticleNucleic acids research2015
RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 58 citations in OpenAlex.
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- 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
- Nucleo-SAFARI: Automated Identification of Fragment Ions in Top-Down MS/MS Spectra of Nucleic Acids.Analytical chemistry · 2024Article
- Unveiling the intricacy of gapmer oligonucleotides through advanced tandem mass spectrometry approaches and scan accumulation for 2DMS.The Analyst · 2024Article
- Analysis of RNA and Its Modifications.Annual review of analytical chemistry (Palo Alto, Calif.) · 2024Review
- MIND4OLIGOS: Determining the Monoisotopic Mass of Oligonucleotides Observed in High-Resolution Mass Spectrometry.Analytical chemistry · 2024Article
- In-Gel Cyanoethylation for Pseudouridines Mass Spectrometry Detection of Bacterial Regulatory RNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Selection of optimised ligands by fluorescence-activated bead sorting.Chemical science · 2023Article
- Challenges and emerging trends in liquid chromatography-based analyses of mRNA pharmaceuticals.Journal of pharmaceutical and biomedical analysis · 2023Review
- Cholesterol Stationary Phase in the Separation and Identification of siRNA Impurities by Two-Dimensional Liquid Chromatography-Mass Spectrometry.International journal of molecular sciences · 2022Article
- Exploring the expanding universe of small RNAs.Nature cell biology · 2022Review
- Advancements in the characterisation of oligonucleotides by high performance liquid chromatography-mass spectrometry in 2021: A short review.Analytical science advances · 2022Review
- Article
- A Compositional Model to Predict the Aggregated Isotope Distribution for Average DNA and RNA Oligonucleotides.Metabolites · 2021Article
- Locating chemical modifications in RNA sequences through ribonucleases and LC-MS based analysis.Methods in enzymology · 2021Article
- Unraveling the RNA modification code with mass spectrometry.Molecular omics · 2020Article
- Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry.Biochimica et biophysica acta. Gene regulatory mechanisms · 2019Review
- Improved application of RNAModMapper - An RNA modification mapping software tool - For analysis of liquid chromatography tandem mass spectrometry (LC-MS/MS) data.Methods (San Diego, Calif.) · 2019Article
- Improving RNA modification mapping sequence coverage by LC-MS through a nonspecific RNase U2-E49A mutant.Analytica chimica acta · 2018Article
- Mapping Post-Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry.Biomolecules · 2017Review
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined 'variable sequencing', which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing.
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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.