Journal
ANALYTICAL CHEMISTRY
Volume 89, Issue 20, Pages 10744-10752Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.analchem.7b01780
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Funding
- National Science Foundation [NSF CHE1507357]
- University of Cincinnati
- Rieveschl Eminent Scholar Endowment
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [1507357] Funding Source: National Science Foundation
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Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven to be a powerful analytical tool for the characterization of modified ribonucleic acids (RNAs). The typical approach for analyzing modified nucleosides within RNA sequences by mass spectrometry involves ribonudease digestion followed by LC-MS/MS analysis and data interpretation. Here we describe a new software tool, RNAMod-Mapper (RAMM), to assist in the interpretation of LC-MS/MS data. RAMM is a stand-alone package that requires user submitted DNA or RNA sequences to create a local database against which collision-induced dissociation (CID) data of modified oligonudeotides can be compared. RAMM can interpret MS/MS data containing modified nucleosides in two modes: fixed and variable. In addition, RAMM can also utilize interpreted MS/MS data for RNA modification mapping back against the input sequence(s). The applicability of RAMM was first tested using total tRNA isolated from Escherichia coli. It was then applied to map modifications found in 16S and 23S rRNA from Streptomyces griseus.
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