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 score

SUBMITTER: Nakayama H 

PROVIDER: S-EPMC2665244 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature