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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/

If you want to use the software with the Gurobi solver (free academic license) instead of GLPK, please follow the instructions in the sirius manual.

Please see the following publications:

Kai Dührkop and Sebastian Böcker. Fragmentation trees reloaded. J Cheminform, 8:5, 2016. (Cite this for fragmentation pattern analysis and fragmentation tree computation)

Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Böcker. Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci U S A, 112(41):12580-12585, 2015. (Cite this when using CSI:FingerID)

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 2.3.0 Documentation generated on Sun Jan 7 2018 03:49:06 using doxygen 1.8.13