How do “same ion” outlines work in Progenesis CoMet?

Each run is aligned and the aligned runs are used to find a common set of compound ion outlines. All of the runs are used during the compound ion detection process so, even if a compound ion is missing from one or more runs, its outline will still be found. This set of outlines is then applied to all aligned runs. This means Progenesis CoMet only measures a zero abundance if the ion is truly missing.