Ariadne: Database Search for RNA Identification Using Tandem Mass Spectrometry Data

Ariadne is updated!

Many functions are revised, and some features requested by users are implemented as below:

  • Known MS2 Fragments -- A new mode of MS/MS dissociation called "Known MS2 Fragments" is supported for improving identification of Part-specific dissociations. For example, unusual, facile losses of m7G base(s) from product ions (c, w, and y) of m7G-containing oligonucleotides can be assigned.
  • Downloading Results -- The calculation/search results can be downloaded in MS Excel .xlsx or text file.
  • Systematic Symbols -- The nomenclature of default Parts is changed for defining synthetic oligonucleotides more easily.
  • Chemical Formulas -- The chemical formulas of precursors and products are shown in result reports.
  • Sequence format -- Termini can be written in FASTA sequences. e.g. OH_ACUG_p

Ariadne is a web-based database search service for the identification of RNAs and their post-transcriptional modifications using tandem mass spectrometry data.If you include results from Ariadne in a publication, please cite the Ariadne paper.


Parts Editor

Mass Calculator

MS/MS Search

Browse demo search results of some of our published data including ribosomal RNA, transfer RNA, microRNA and other non-coding RNAs and more. Download and try example MS/MS data to search RNA sequence databases by yourself.

Searching an RNA sequence database (up to 50MB) with post-transcriptional modifications using up to 50MB of MS/MS data in Mascot generic format (MGF).

A result report can be browsed with 'search ID' issued on the time of search.


Calculating mass values of a nucleic acid, its RNase digests and their CID fragments from given sequence(s).

Defining/editing user nucleotide parts such as Nucleosides, Linkers, and Termini as well as unusual part-specific MS/MS dissociations.

Table of the available parts that can be used in a calculation/search.