title: Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data.
abstract: 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 tRNA(Phe-1).
authors.affiliation: Biomolecular Characterization Team, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Nakayama
authors.forename: Misaki
authors.initials: M
authors.lastname: Akiyama
authors.forename: Masato
authors.initials: M
authors.lastname: Taoka
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Yamauchi
authors.forename: Yuko
authors.initials: Y
authors.lastname: Nobe
authors.forename: Hideaki
authors.initials: H
authors.lastname: Ishikawa
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Takahashi
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Isobe
mesh_terms: D001483:Base Sequence; D030561:Databases, Nucleic Acid; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D012313:RNA / Q000737:chemistry*; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000737:chemistry; D012360:RNA, Transfer, Phe / Q000737:chemistry / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D012333:RNA, Messenger; D012360:RNA, Transfer, Phe; D022661:RNA, Untranslated; D012313:RNA