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

Nakayama H, Akiyama M, Taoka M, Yamauchi Y, Nobe Y, Ishikawa H, Takahashi N, Isobe T - Nucleic Acids Res. (2009)

Bottom Line: 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).

View Article: PubMed Central - PubMed

Affiliation: Biomolecular Characterization Team, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan.

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).

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Schematic diagram of the Ariadne database search program. Ariadne evaluates tandem MS data of nucleolytic fragments of RNA using a unique two-step algorithm, ‘MS/MS ion search’ and ‘nucleotide mapping’. See text for details.
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Figure 1: Schematic diagram of the Ariadne database search program. Ariadne evaluates tandem MS data of nucleolytic fragments of RNA using a unique two-step algorithm, ‘MS/MS ion search’ and ‘nucleotide mapping’. See text for details.

Mentions: We designed the software Ariadne to assign a particular RNA identity by searching a set of MS/MS data resulting from the fragments produced by limited nucleolytic cleavage against a DNA/RNA database. Figure 1 illustrates the outline of the Ariadne search algorithm. To specify a particular RNA with limited MS/MS data from huge numbers of potential RNA species in the database, Ariadne evaluates the MS data in two steps. In the first ‘MS/MS ion searching’ step, the software compares the peak list extracted from raw MS data of a sample RNA and its RNase fragments with those obtained by in silico nuclease digestion of all RNA entries in the sequence database, evaluates the data matching by a quantitative score and selects candidate oligoribonucleotide(s). In general, however, a single oligonucleotide fragment produced by RNase digestion is assigned to multiple RNA entries in the database and cannot be used to specify a single RNA species. Thus in the second ‘nucleotide mapping’ step, Ariadne maps a set of nucleotide fragments identified in the sample RNA on all RNA entries in the database, evaluates the density of localization by a probability-based score and finds the RNA species with the highest score. It should be noted that these two evaluation steps were necessary for reliable RNA identification, essentially because RNA has fewer variable constituents than protein (4 versus 20) and thereby has a decreased likelihood of producing a unique fragment that can be attributed to a single RNA species upon RNase digestion. In addition, RNA is transcribed from relatively wide, undefined regions of the genome, whereas proteins are encoded by genes, which occur within relatively narrow, defined regions of the genome (see ‘Discussion’ section).Figure 1.


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

Nakayama H, Akiyama M, Taoka M, Yamauchi Y, Nobe Y, Ishikawa H, Takahashi N, Isobe T - Nucleic Acids Res. (2009)

Schematic diagram of the Ariadne database search program. Ariadne evaluates tandem MS data of nucleolytic fragments of RNA using a unique two-step algorithm, ‘MS/MS ion search’ and ‘nucleotide mapping’. See text for details.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2665244&req=5

Figure 1: Schematic diagram of the Ariadne database search program. Ariadne evaluates tandem MS data of nucleolytic fragments of RNA using a unique two-step algorithm, ‘MS/MS ion search’ and ‘nucleotide mapping’. See text for details.
Mentions: We designed the software Ariadne to assign a particular RNA identity by searching a set of MS/MS data resulting from the fragments produced by limited nucleolytic cleavage against a DNA/RNA database. Figure 1 illustrates the outline of the Ariadne search algorithm. To specify a particular RNA with limited MS/MS data from huge numbers of potential RNA species in the database, Ariadne evaluates the MS data in two steps. In the first ‘MS/MS ion searching’ step, the software compares the peak list extracted from raw MS data of a sample RNA and its RNase fragments with those obtained by in silico nuclease digestion of all RNA entries in the sequence database, evaluates the data matching by a quantitative score and selects candidate oligoribonucleotide(s). In general, however, a single oligonucleotide fragment produced by RNase digestion is assigned to multiple RNA entries in the database and cannot be used to specify a single RNA species. Thus in the second ‘nucleotide mapping’ step, Ariadne maps a set of nucleotide fragments identified in the sample RNA on all RNA entries in the database, evaluates the density of localization by a probability-based score and finds the RNA species with the highest score. It should be noted that these two evaluation steps were necessary for reliable RNA identification, essentially because RNA has fewer variable constituents than protein (4 versus 20) and thereby has a decreased likelihood of producing a unique fragment that can be attributed to a single RNA species upon RNase digestion. In addition, RNA is transcribed from relatively wide, undefined regions of the genome, whereas proteins are encoded by genes, which occur within relatively narrow, defined regions of the genome (see ‘Discussion’ section).Figure 1.

Bottom Line: 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).

View Article: PubMed Central - PubMed

Affiliation: Biomolecular Characterization Team, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan.

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).

Show MeSH