ArticleNucleic acids research2009
Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 44 citations in OpenAlex.
- Characterization and Sequence Mapping of Large RNA and mRNA Therapeutics Using Mass Spectrometry.Analytical chemistry · 2022Article
- Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine.Chemical science · 2021Review
- Unraveling the RNA modification code with mass spectrometry.Molecular omics · 2020Article
- 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
- Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry.Biochimica et biophysica acta. Gene regulatory mechanisms · 2019Review
- High resolution fingerprinting of single and double-stranded RNA using ion-pair reverse-phase chromatography.Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2019Article
- Mapping Post-Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry.Biomolecules · 2017Review
- Purification and characterisation of dsRNA using ion pair reverse phase chromatography and mass spectrometry.Journal of chromatography. A · 2017Article
- Article
- Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry.Methods (San Diego, Calif.) · 2016Article
- Mass spectrometry of modified RNAs: recent developments.The Analyst · 2016Review
- RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids.Nucleic acids research · 2015Article
- Metabolic de-isotoping for improved LC-MS characterization of modified RNAs.Journal of the American Society for Mass Spectrometry · 2014Article
- The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry.RNA biology · 2014Review
- Intact microRNA analysis using high resolution mass spectrometry.Journal of the American Society for Mass Spectrometry · 2014Article
- Relative quantitation of transfer RNAs using liquid chromatography mass spectrometry and signature digestion products.Nucleic acids research · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The idea of identifying or characterizing an RNA molecule based on a mass spectrum of specifically generated RNA fragments has been used in various forms for well over a decade. We have developed software-named RRM for 'RNA mass mapping'-which can search whole prokaryotic genomes or RNA FASTA sequence databases to identify the origin of a given RNA based on a mass spectrum of RNA fragments. As input, the program uses the masses of specific RNase cleavage of the RNA under investigation. RNase T1 digestion is used here as a demonstration of the usability of the method for RNA identification. The concept for identification is that the masses of the digestion products constitute a specific fingerprint, which characterize the given RNA. The search algorithm is based on the same principles as those used in peptide mass fingerprinting, but has here been extended to work for both RNA sequence databases and for genome searches. A simple and powerful probability model for ranking RNA matches is proposed. We demonstrate viability of the entire setup by identifying the DNA template of a series of RNAs of biological and of in vitro transcriptional origin in complete microbial genomes and by identifying authentic 16S ribosomal RNAs in a 'small ribosomal subunit RNA' database. Thus, we present a new tool for a rapid identification of unknown RNAs using only a few picomoles of starting material.
Indexed as
Identifiers
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.