Tools to convert between different file formats that are related to MetFrag’s usage.

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Massbank to MetFrag

Convert a Massbank record to a MetFrag query file to directly process it with MetFrag.

# java -jar ConvertMassbankToMetFragRecord.jar massbank-input-file metfrag-output-file

The converter writes information extracted from the Massbank record in the MetFrag query file. This includes among other things the given peak list as well as the precursor mass and if available the molecular formula and database identifiers of the relating molecule.


Convert a SDF output file generated by MetFrag to the more human-readable XLS file format.

# java -jar ConvertSDFtoXLS.jar sdf-input-file output-folder
# java -jar ConvertSDFtoXLS.jar sdf-input-file output-folder 1 //with images

The defined output folder is used to mark the destination for the gernerated XLS output file that will contain the given SDF properties in seperate columns. If the additional third parameter 1 is given, the converter generates structure images that are displayed in an extra column for each molecule. This option is not recommended if the SDF contains a large number of candidates.