We introduce OrbiFragsNets, a tool for automatic annotation of MS2 spectra generated by Orbitrap instruments, as well as the concepts of chemical consistency and fragments networks. OrbiFragsNets takes advantage of the specific confidence interval for each peak in every MS2 spectrum, which is an unclear idea across the high-resolution mass spectrometry literature. The spectrum annotations are expressed as fragments networks, a set of networks with the possible combinations of annotations for the fragments. The model behind OrbiFragsNets is briefly described here and explained in detail in the constantly updated manual available in the GitHub repository. This new approach in MS2 spectrum de novo automatic annotation proved to perform as good as well established tools such as RMassBank and SIRIUS.
•A new approach on automatic annotation of Orbitrap MS2 spectra is introduced.
•Possible spectrum annotation are described as independent consistent networks, with annotations for each fragment as nodes, and annotations for the mass difference between fragments as edges.
•Annotation process is described as the selection of the most connected fragments network.