Extended Data Fig. 4: precisION’s fragment- level open search can detect a diverse range of fragment ion modifications without constraint.

Schematic overview of the fragment-level open search. In a first pass search, observed ions are assigned to unmodified sequence ions. After this search, the residual unassigned ions are assumed to mainly consist of modified sequence ions. To identify these modifications, a mass offset is applied to each of the theoretical sequence ions, then the number of matches between the observed ions and the offset theoretical ions is counted. By scanning across a continuous range of mass offsets using a sliding window approach, the algorithm can identify offsets that produce a significantly high number of matches. Peaks in this scan indicate sets of sequence ions with a common modification. Here an example mass offset of +79.965 is shown to result in an increased number of matches compared to the background. Searching for this mass offset in UniMod would suggest it to correspond to a set of phosphorylated sequence ions.