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AssayGeneratorMetabo

Generates an assay library using DDA data (Metabolomics)

potential predecessor tools → AssayGeneratorMetabo → potential successor tools
FeatureFinderMetabo OpenSWATH pipeline
AccurateMassSearch

Build an assay library from DDA data (MS and MS/MS) (mzML). Please provide a list of features found in the data (featureXML).

Features can be detected using the FeatureFinderMetabo (FFM) and identifcation information can be added using the AccurateMassSearch featureXML output.

If the FeatureFinderMetabo featureXML does not contain any identifications the "use_known_unknowns" flag is used automatically.

Internal procedure AssayGeneratorMetabo:

  1. Input mzML and featureXML
  2. Reannotate precursor mz and intensity
  3. Filter feature by number of masstraces
  4. Assign precursors to specific feature (FeatureMapping)
  5. Extract feature meta information (if possible)
  6. Find MS2 spectrum with highest intensity precursor for one feature
  7. Annotation is performed either the MS2 with the highest intensity precursor or a consensus spectrum can be used for the transition extraction.
  8. Calculate thresholds (maximum and minimum intensity for transition peak)
  9. Extract and write transitions (tsv, traml)

The command line parameters of this tool are:

INI file documentation of this tool: