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Nucleic Acids Research Advance Access published online on March 6, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp099
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© 2009
The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data

Hiroshi Nakayama1,2, Misaki Akiyama1,2, Masato Taoka3, Yoshio Yamauchi3, Yuko Nobe2,3, Hideaki Ishikawa2,4, Nobuhiro Takahashi2,4 and Toshiaki Isobe2,3,*

1Biomolecular Characterization Team, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, 2Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, 3Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397 and 4Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan

*To whom correspondence should be addressed. Tel: +81 42 677 2542; Fax: +81 42 677 2525; Email: isobe-toshiaki{at}tmu.ac.jp

Received December 26, 2008. Revised February 3, 2009. Accepted February 7, 2009.

We present here a method to correlate tandem mass spectra of sample RNA nucleolytic fragments with an RNA nucleotide sequence in a DNA/RNA sequence database, thereby allowing tandem mass spectrometry (MS/MS)-based identification of RNA in biological samples. Ariadne, a unique web-based database search engine, identifies RNA by two probability-based evaluation steps of MS/MS data. In the first step, the software evaluates the matches between the masses of product ions generated by MS/MS of an RNase digest of sample RNA and those calculated from a candidate nucleotide sequence in a DNA/RNA sequence database, which then predicts the nucleotide sequences of these RNase fragments. In the second step, the candidate sequences are mapped for all RNA entries in the database, and each entry is scored for a function of occurrences of the candidate sequences to identify a particular RNA. Ariadne can also predict post-transcriptional modifications of RNA, such as methylation of nucleotide bases and/or ribose, by estimating mass shifts from the theoretical mass values. The method was validated with MS/MS data of RNase T1 digests of in vitro transcripts. It was applied successfully to identify an unknown RNA component in a tRNA mixture and to analyze post-transcriptional modification in yeast tRNAPhe-1.


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M. Taoka, Y. Yamauchi, Y. Nobe, S. Masaki, H. Nakayama, H. Ishikawa, N. Takahashi, and T. Isobe
An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes
Nucleic Acids Res., November 1, 2009; 37(21): e140 - e140.
[Abstract] [Full Text] [PDF]


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