EDITORIAL: THE STUDY OF RIBONUCLEOPROTEOMICS WITHMASS SPECTROMETRY (MS)-BASED TECHNOLOGY

Mass spectrometry (MS) is one of the most powerful analytical methods to characterizephysiologically active substances. The advent of MS analyzers and ionization sources made itpossible to rapidly determine the elemental composition of macromolecules such as peptides andproteins. Coupled with other techniques, including nanoliter-scale liquid chromatography, we canidentify with high resolution and sensitivity almost any protein in a proteome; that is, the entireprotein entity expressed in a cell, tissue, or organism. Furthermore, we are able to characterize post-translational modifications of proteins on a large scale. Combined with sophisticated proteinpreparation methods, such as tandem affinity purification or activity-based protein profiling, MS-based technology has greatly enlarged the field of proteomics, so much so that it is now a majorinterdisciplinary research area of life science in the post-genomic era.

In the meantime, a large proportion of the genomewas found to produce non-coding RNAs that arenot translated into proteins. For instance, only approximately 1.5% of the entire human genomeencodes coding RNAs that are translated into proteins, whereas no less than 40% give rise to non-codingRNAs.Moreover, non-codingRNAs play pivotal roles in a variety of cellular processes, suchas transcriptional regulation, RNA processing, gene silencing, and translational regulation. In mostcases, non-coding RNAs form ribonucleoprotein (RNP) complexes with proteins and act onendonucleolytic RNA cleavage and ligation, site-specific RNAmodulation, DNAmethylation, etc.Because post-transcriptionalmodifications of tRNAs and rRNAs are prevalent and essential for theirbiogenesis and function, they probably are present in other non-codingRNAs aswell. RNAs are alsosubject to metabolic degradation and biochemical reactions in vivo.

To date, non-coding RNAs have been analyzed mostly by techniques based on molecular biologyand RNA biochemistry. Although those conventional techniques are undoubtedly useful tocharacterize various aspects of RNA, they depend on the error-prone process of reverse transcriptionfrom RNA to cDNA before the nucleic acid sequences can be determined, and they fail to provideinformation on post-transcriptional modifications of nucleosides. For unbiased characterization ofnon-coding RNAs, it is desirable to carry out direct analyses of RNAs extracted from biologicalsamples, without recourse to reverse transcription. Because conventional techniques do not admit tothe rectification of these shortcomings, we need to develop a novel method of direct chemicalanalysis that can characterize RNAs for post-transcriptional modifications and any changes thatresult from metabolic degradation and biochemical reactions; that method must possess sensitivityand throughput at least as high as those used in proteomics. MS-based technology fully satisfies therequired conditions; it directly measures the intrinsic mass of RNAs, provides unparalleledspecificity, and allows quantification and identification of RNAs together with their impurities andmetabolites. As MS offers high sensitivity for the direct chemical analysis of RNA, it is an idealmethod for complementing conventional techniques.

We thus consider it timely to devote a couple of special issues of Mass Spectrometry Reviews toMS analysis of non-coding RNAs. In this present first issue, we focus on the MS-analysis of thesmall interference RNAs (siRNAs) that are synthesized for therapeutic purposes. siRNA is a short(19–22 bp) double-stranded RNA (dsRNA), and is chemically modified to prevent nucleasedegradation so as to improve pharmacokinetic properties. The biological function of siRNAresembles that ofmicroRNA(miRNA); both suppress expression of certain genes through activationof the intrinsic RNA interference (RNAi) pathway that results in mRNA cleavage. In this pathway,siRNA or miRNA in duplex form is unwound to become single-stranded and loaded onto a proteincomplex called RISC (RNA-induced silencing complex). siRNAdiffers frommiRNA in that siRNAis introduced into cells from exogenous sources, whereas miRNA is produced intrinsically from itsendogenous dsRNA precursor in the nucleus. Because siRNA enables us to manipulate genefunction exogenously, it became widely used in standard laboratory procedures of basic research

Mass Spectrometry Reviews, 2011, 30, 977– 978# 2009 by Wiley Periodicals, Inc.

Published online 4 November 2009 in Wiley Online Library (wileyonlinelibrary.com).

DOI 10.1002/mas.20274

and, perhaps more importantly, has received a lot of publicity because of possible therapeuticapplications. siRNA serves as an excellent model because it provides many technological aspectsassociated with MS analysis of RNAs extracted from biological samples. Beverly expertlysummarizes MS-based analysis of siRNAs from basic and practical viewpoints.

Nobuhiro TakahashiApplied Biological ScienceTokyo University of Agriculture & Technology3-5-8 Saiwai-Cho, Fuchu-ShiTokyo 183-8509E-mail: ntakahas@cc.tuat.ac.jp

& TAKAHASHI

978 Mass Spectrometry Reviews DOI 10.1002/mas