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AssayGeneratorMetaboSirius

Generates an assay library from SIRIUS fragmentation trees (Metabolomics)

potential predecessor tools → AssayGeneratorMetaboSirius → potential successor tools
FeatureFinderMetabo OpenSWATH pipeline
AccurateMassSearch
SiriusExport

Build an assay library from a SIRIUS project directory using fragmentation trees.

  • Use the SiriusExport TOPP tool with each samples mzML and featureXML files to generate a SIRIUS input ms file.
    SiriusExport -in sample.mzML -in_featureinfo sample.featureXML -out_ms sample.ms
  • Run SIRIUS externally with "--no-compression" flag and the formula, passatutto (optional, for decoy generation) and write-summaries tools.
  • This tool was tested with the SIRIUS project directory generated with SIRIUS versions >= 5.5.1 and <= 5.8.6.
    sirius --input sample.ms --project sirius-project --maxmz 300 --no-compression formula passatutto write-summaries
  • Provide the path to SIRIUS project as input parameter for this tool.

The command line parameters of this tool are:

INI file documentation of this tool: