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.
InChI strings need to start with "InChI=" and are not expected to have any charge - an additional H+ will be added. Maximum compound size is 200 atoms.

The spectra should be represented as a list of peaks with the format 'mass intensity' on each line, and can be entered directly into the corresponding energy level boxes below. Only centroided spectrum can be entered. Multiple energy levels are optional; only one is required.

The spectra should be represented as a list of peaks with the format 'mass intensity' on each line. For ESI spectra, 'low','medium', and 'high' or 'energy0', 'energy1', and 'energy2' header lines should begin spectra of different energy levels (in that order) and multiple energy levels are optional (only one is required). EI spectra only need to have one energy level. Spectra may also be in .msp file format, in which case energy levels for ESI spectra should be specified in the "Comment: " field (EI spectra do not need a specified energy level). A corresponding spectra ID must be selected for .msp spectra. See an example peak list file or an example .msp file.

* required for .msp files only

The mass tolerance to use when matching peaks within the spectrum comparison.

Please wait while your input is validated (this may take a few seconds)
If you wish to run multiple jobs, input larger query molecules, or customize the computation parameters, you can freely download the docker image.