Annotates the peaks in a provided set of spectra given a known molecule. The complete list of feasible fragments is computed, then the most likely fragments for each spectrum peak are determined using a pre-trained SE-CFM model. The results provide an annotated form of the original spectra, with each peak appended with a list of ids corresponding to any fragments with the correct mass, listed in order from most to least likely. A hypothesized fragmentation graph is also provided, which contains all annotated fragments and the possible paths by which they could have been produced. This is provided in the form of a list of fragments and a list of transitions between those fragments.
If you wish to run multiple jobs, input larger query molecules, or customize the computation parameters, you can freely download the source code here: http://sourceforge.net/projects/cfm-id.