ssmehta

CFM-ID is a set of utilities "associated with the interpretation of tandem mass spectra (MS/MS)."

MAGMa+ is a wrapper around the MAGMa metabolite identification with dynamic parameter selection.

MAGMa is an tool for "automatic chemical annotation of accurate multistage MS^n spectral data."

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.