This function annotates the fragment ion peaks in a given MS/MS spectra for a given molecule. Users must provide a chemical structure (SMILES or InChI) and a spectral peak list from an MS/MS experiment. Once the data are submitted, a complete list of feasible fragments is computed by CFM-ID, 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 submitted experimental 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 the 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 docker image.