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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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Mapping score histogram of the xCyPA mRNA search results. Scores for all entries in the database are summarized in the histogram. Frequencies of entries within a 10-point scoring range were counted, converted to common logarithm of frequency +1 and plotted. Note that the histogram shows a ‘hit’ for the query, as indicated by a distinctly high score.
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Figure 4: Mapping score histogram of the xCyPA mRNA search results. Scores for all entries in the database are summarized in the histogram. Frequencies of entries within a 10-point scoring range were counted, converted to common logarithm of frequency +1 and plotted. Note that the histogram shows a ‘hit’ for the query, as indicated by a distinctly high score.

Mentions: Ariadne has a unique second-step evaluation algorithm called ‘nucleotide mapping’, whereby a set of oligonucleotide fragments identified in the first ‘MS/MS ion-searching’ step is mapped on all RNA entries in the database. Ariadne then evaluates the density of the oligonucleotide localization by a probability-based score and presents the RNA species with the highest score. To assess the performance of this ‘nucleotide mapping’ procedure, all oligonucleotide fragments containing both 62 correct and 74 incorrect sequences derived from the analysis of xCyPA mRNA (Supplementary Table S1) were mapped on all entries in the merged database. Each entry was scored, and the entries were then sorted by this score in descending order. As shown by the histogram in Figure 4, the xCyPA mRNA sequence was easily singled out because of its significantly higher score from all other entries in the database, which consisted of sequences numbering in the several tens of thousands. Thus, the two-step scoring algorithm of Ariadne provided confident identification of a single RNA species from among a large number of potential candidate RNAs in a database.Figure 4.


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)

Mapping score histogram of the xCyPA mRNA search results. Scores for all entries in the database are summarized in the histogram. Frequencies of entries within a 10-point scoring range were counted, converted to common logarithm of frequency +1 and plotted. Note that the histogram shows a ‘hit’ for the query, as indicated by a distinctly high score.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: Mapping score histogram of the xCyPA mRNA search results. Scores for all entries in the database are summarized in the histogram. Frequencies of entries within a 10-point scoring range were counted, converted to common logarithm of frequency +1 and plotted. Note that the histogram shows a ‘hit’ for the query, as indicated by a distinctly high score.
Mentions: Ariadne has a unique second-step evaluation algorithm called ‘nucleotide mapping’, whereby a set of oligonucleotide fragments identified in the first ‘MS/MS ion-searching’ step is mapped on all RNA entries in the database. Ariadne then evaluates the density of the oligonucleotide localization by a probability-based score and presents the RNA species with the highest score. To assess the performance of this ‘nucleotide mapping’ procedure, all oligonucleotide fragments containing both 62 correct and 74 incorrect sequences derived from the analysis of xCyPA mRNA (Supplementary Table S1) were mapped on all entries in the merged database. Each entry was scored, and the entries were then sorted by this score in descending order. As shown by the histogram in Figure 4, the xCyPA mRNA sequence was easily singled out because of its significantly higher score from all other entries in the database, which consisted of sequences numbering in the several tens of thousands. Thus, the two-step scoring algorithm of Ariadne provided confident identification of a single RNA species from among a large number of potential candidate RNAs in a database.Figure 4.

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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