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SiriusExport

De novo metabolite identification.

Exports an input file for SIRIUS, a tool for metabolomics data analysis with several subtools, each serving specific purposes:

  • SIRIUS: Identify molecular formula for each compound individually using fragmentation trees and isotope patterns. Output from this tool can be used to generate an OpenSwathAssay library with the AssayGeneratorMetabo TOPP tool.
  • CSI:FingerID: This subtool is dedicated to predicting molecular structures based on tandem mass spectrometry (MS/MS) data. It utilizes a fragmentation tree approach for the annotation of fragment spectra.
  • CANOPUS: Predict compound categories for each compound individually based on its predicted molecular fingerprint (CSI:FingerID) using CANOPUS.
  • Passatutto: Compute decoy spectra based on the fragmentation trees of the given input spectra. If no molecular formula is provided in the input, the top scoring computed formula is used. Required to include decoys in an OpenSwathWorkflow assay library generated by the AssayGeneratorMetabo TOPP tool.

Sirius can be found at https://bio.informatik.uni-jena.de/software/sirius/

Internal procedure in SiriusExport

  1. Input mzML (and optional featureXML)
    Make sure to input the matching mzML and featureXML files in the correct order.
  2. Preprocessing
    By providing a featureXML, the feature information can be used for feature mapping.
    Sirius will then process the internally merged MS2 spectra allocated to one feature (instead of all available MS2).
    To reduce the feature space even further a masstrace filter can be set.
    Additional adduct information can be provided using a featureXML from the MetaboliteAdductDecharger or AccurateMassSearch.
  3. Parsed by SiriusMSConverter into (sirius internal) .ms format

The command line parameters of this tool are:

INI file documentation of this tool: