Extended Data Fig. 3: Continuous MS2 acquisition resolves co-eluting ionic species by comparing their fragment elution profile.

a) All fragment ions from continuous MS2 scans are grouped according to their m/z. b) A loose peak-picking algorithm is applied and the resulting peaks are grouped according to their elution profiles, generating a similarity network that is split by a greedy clustering algorithm. c) This grouping yields a curated MS2 spectra for each coeluting species (see Algorithm 3). (*) The shaded slice shows the impact of the algorithm on the resulting MS2 spectral quality. The delineated fragments in blue have a different elution pattern from the rest and would contaminate the MS2 spectra if only one scan was acquired at the top of the peak. The grouping performed by HERMES confidently removes the contaminant ions and separates each group of fragments according to their elution.