Skip Navigation


Nucleic Acids Research Advance Access originally published online on March 6, 2009
Nucleic Acids Research 2009 37(6):e47; doi:10.1093/nar/gkp099
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (244K) Freely available
Right arrow Screen PDF (231K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
37/6/e47    most recent
gkp099v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Nakayama, H.
Right arrow Articles by Isobe, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Nakayama, H.
Right arrow Articles by Isobe, T.
Related Collections
Right arrow RNA characterisation and manipulation
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2009, Vol. 37, No. 6 e47
© 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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
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., September 9, 2009; (2009) gkp732v1.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.