Limits...
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).

Show MeSH

Related in: MedlinePlus

Low-energy CID pattern of deprotonated ion of RNA. The fragmentation pattern is illustrated by an oligoribonucleotide with a sequence 5′-OH-CUAG-cyclic-phosphate-3′. The nomenclature of sequence ions is in accordance with McLuckey et al. (26). The structures of c/y ions are according to Tromp and Schuerch (37). The tentative structures of internal fragment ions produced by the double-backbone cleavage are designated as i(AU) and i(AU+p) for the structural variants shown in the figure. In this example, i(AU) contains two isomers that cannot be discriminated according to their mass.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2665244&req=5

Figure 2: Low-energy CID pattern of deprotonated ion of RNA. The fragmentation pattern is illustrated by an oligoribonucleotide with a sequence 5′-OH-CUAG-cyclic-phosphate-3′. The nomenclature of sequence ions is in accordance with McLuckey et al. (26). The structures of c/y ions are according to Tromp and Schuerch (37). The tentative structures of internal fragment ions produced by the double-backbone cleavage are designated as i(AU) and i(AU+p) for the structural variants shown in the figure. In this example, i(AU) contains two isomers that cannot be discriminated according to their mass.

Mentions: To implement the MS/MS spectral information of oligoribonucleotides into Ariadne, we studied low-energy CID profiles of multiple charged negative ions of synthetic RNAs generated by ESI (Taoka,M. et al., manuscript in preparation). As noted previously by Schuerch et al. (27) and Tromp and Schuerch (37), we detected mainly the c/y series of product ions and the w1 ion in many CID spectra, as well as weaker signals of a/w ions. We also observed internal fragment ions that arose from double-backbone fragmentation and fragment ions that had lost nucleotide bases. Although the nomenclature of internal fragment ions has not yet been defined, we tentatively assigned those ions in our search engine as shown in Figure 2. Thus, we implemented the assignments of a, c, w and y series of sequence ions, the internal fragmentation ions and base loss from the molecular ions into our search engine Ariadne (Figure 2).Figure 2.


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)

Low-energy CID pattern of deprotonated ion of RNA. The fragmentation pattern is illustrated by an oligoribonucleotide with a sequence 5′-OH-CUAG-cyclic-phosphate-3′. The nomenclature of sequence ions is in accordance with McLuckey et al. (26). The structures of c/y ions are according to Tromp and Schuerch (37). The tentative structures of internal fragment ions produced by the double-backbone cleavage are designated as i(AU) and i(AU+p) for the structural variants shown in the figure. In this example, i(AU) contains two isomers that cannot be discriminated according to their mass.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Low-energy CID pattern of deprotonated ion of RNA. The fragmentation pattern is illustrated by an oligoribonucleotide with a sequence 5′-OH-CUAG-cyclic-phosphate-3′. The nomenclature of sequence ions is in accordance with McLuckey et al. (26). The structures of c/y ions are according to Tromp and Schuerch (37). The tentative structures of internal fragment ions produced by the double-backbone cleavage are designated as i(AU) and i(AU+p) for the structural variants shown in the figure. In this example, i(AU) contains two isomers that cannot be discriminated according to their mass.
Mentions: To implement the MS/MS spectral information of oligoribonucleotides into Ariadne, we studied low-energy CID profiles of multiple charged negative ions of synthetic RNAs generated by ESI (Taoka,M. et al., manuscript in preparation). As noted previously by Schuerch et al. (27) and Tromp and Schuerch (37), we detected mainly the c/y series of product ions and the w1 ion in many CID spectra, as well as weaker signals of a/w ions. We also observed internal fragment ions that arose from double-backbone fragmentation and fragment ions that had lost nucleotide bases. Although the nomenclature of internal fragment ions has not yet been defined, we tentatively assigned those ions in our search engine as shown in Figure 2. Thus, we implemented the assignments of a, c, w and y series of sequence ions, the internal fragmentation ions and base loss from the molecular ions into our search engine Ariadne (Figure 2).Figure 2.

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
Related in: MedlinePlus