Fig. 3

Analysis Workflow. After importing the tandem mass spectra of a compound, all molecular formulas within the mass accuracy of the parent peak are generated (3). Each of these candidates is then scored (4–7) and, finally, candidates are sorted with respect to this score (8). To score a candidate molecular formula, we compute the fragmentation graph with the candidate formula being the root (4); score the edges of the graph using Bayesian statistics (5); find the best-scoring FT in this graph using combinatorial optimization (6); finally, we use hypothesis-driven recalibration to find a best match between theoretical and observed peak masses (7), recalibrate, and repeat steps (4–6) for this candidate formula. In our evaluation, we compare the output list with the true answer (9)