Characterization of Ribonucleic Acids and Their Modifications by Fourier Transform Ion Cyclotron Resonance Mass Spectrom
Recent advances in electrospray ionization and the extension of radical ion based dissociation techniques to ribonucleic acids (RNA) were key factors for developing top-down mass spectrometry as a powerful method for the detailed characterization of postt
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Characterization of Ribonucleic Acids and Their Modifications by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Kathrin Breuker
Abstract
Recent advances in electrospray ionization and the extension of radical ion based dissociation techniques to ribonucleic acids (RNA) were key factors for developing top-down mass spectrometry as a powerful method for the detailed characterization of posttranscriptional and synthetic modifications of RNA. This new approach identifies and localizes all mass-altering modifications without the need for labeling reactions, and can be used for characterization of RNA of unknown sequence. Keywords
RNA • Posttranscriptional modifications • Synthetic modifications • Collisionally activated dissociation • Electron detachment dissociation • Top-down mass spectrometry • Fourier transform ion cyclotron resonance • Mass spectrometry
Abbreviations/Formulae BIRD CAD CID cDNA DNA ECD EDD EPD ESI
Blackbody infrared multiphoton dissociation Collisionally activated dissociation (synonymous with CID) Collision-induced dissociation (synonymous with CAD) Complementary desoxyribonucleic acid Desoxyribonucleic acid Electron capture dissociation Electron detachment dissociation Electron photodetachment dissociation Electrospray ionization
K. Breuker (*) Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, CCB, Innrain 80/82, 6020 Innsbruck, Austria e-mail: [email protected] V. Gabelica (ed.), Nucleic Acids in the Gas Phase, Physical Chemistry in Action, DOI 10.1007/978-3-642-54842-0_7, # Springer-Verlag Berlin Heidelberg 2014
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FTICR IRMPD MALDI MS nETD nt PTM RNA siRNA tRNA
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K. Breuker
Fourier transform ion cyclotron resonance Infrared multiphoton dissociation Matrix-assisted laser desorption/ionization Mass spectrometry Negative electron transfer dissociation Nucleotide(s) Posttranscriptional modification Ribonucleic acid Small interfering RNA Transfer RNA
Introduction
In living organisms, the genetic information encoded in desoxyribonucleic acids (DNA) is transcribed only in part into ribonucleic acids (RNA) by RNA polymerases, and only a fraction of the RNA is translated into proteins at the ribosome. This protein fraction is stunningly small in homo sapiens, 10 eV) electrons that, depending on experimental factors such as electron energy and density, cause detachment of one or more electrons from the (M nH)n ions. Because radiofrequency fields and higher background pressures in mass spectrometers other than FTICR instruments severely limit electron mean free paths, EDD is restricted to FTICR MS. However, the recently developed methods negative electron transfer dissociation (nETD) [65–68] and electron photodetachment dissociation (EPD) [69–73] can also produce (M nH)(n1)• from (M nH)n ions, but further studies are needed to evaluate possible differences between fragmentation mechanisms in EDD, nETD, and EPD, especially for RNA. The first study on EDD of (M nH)n ions of RNA, which consis
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