An MS/MS Shortlist Is Not an Identification: Choosing a Formula-Free Ranker and Knowing When to Decline
On MassSpecGym formula split seed 1 (10,648 test spectra from 1,421 molecules, [M+H]+ and [M+Na]+ only), two trained alignment models put the true structure in a five-structure shortlist for 61.4% and 63.2% of spectra, against 13.3% for precursor mass error. Their top scores are only a weak signal that the answer is missing.
