De novo metabolite identification.
CSI:FingerID (Compound Structure Identification: FingerID) is a method for searching a tandem mass spectrum of a small molecule (metabolite) in a database of molecular structures.
To use this feature, the Sirius command line tool as well as a java installation is needed.
Sirius can be found on https://bio.informatik.uni-jena.de/software/sirius/
Please use Sirius Version 4.0.1
If you want to use the software with the Gurobi solver or CPLEX instead of GLPK, please follow the instructions in the sirius manual.
Internal procedure in SiriusAdapter
- Input mzML (and optional featureXML)
- Preprocessing (see below)
- Parsed by SiriusMSConverter into (sirius internal) .ms format
- Submission of .ms and additional parameters to wrapped SIRIUS CLI
- Sirius output saved in internal temporary folder structure
- Sirius output is parsed (SiriusMzTabWriter/CsiFingerIDMzTabWriter)
- Merge corresponding output in one mzTab (out_sirius/out_fingerid)
Preprocessing (featureXML): 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.
The command line parameters of this tool are:
INI file documentation of this tool: