title: The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry.
abstract: The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems.
authors.affiliation: a Rieveschl Laboratories for Mass Spectrometry; Department of Chemistry ; University of Cincinnati ; Cincinnati , OH USA.
authors.forename: Kirk W
authors.initials: KW
authors.lastname: Gaston
authors.forename: Patrick A
authors.initials: PA
authors.lastname: Limbach
mesh_terms: D001483:Base Sequence; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009705:Nucleosides / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D009841:Oligonucleotides / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D034741:RNA, Small Interfering / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D022661:RNA, Untranslated / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D013822:Thermoplasma / Q000235:genetics / Q000378:metabolism
chemical_list: D009705:Nucleosides; D009841:Oligonucleotides; D012333:RNA, Messenger; D012338:RNA, Ribosomal, 23S; D034741:RNA, Small Interfering; D022661:RNA, Untranslated
keywords: LC-MS/MS; MALDI-MS/MS; RNA sequencing; biological ribonucleic acids; modified RNA; modified bases; rRNA; tRNA; tandem mass spectrometry