FingerID
Metabolite identification via machine learning.
...FingerID since version 1.4 will be hosted on github: https://github.com/icdishb/fingerid
A metabolite identification software using tandem mass spectrometry and kernel methods. The related paper can be found at http://bioinformatics.oxfordjournals.org/content/early/2012/07/18/bioinformatics.bts437.abstract.
Now it supports unix/linux like system.