How do "same peptide" outlines work in Progenesis LC-MS?
Each run is aligned and the aligned runs are used to find a common set of peptide outlines. All of the runs are used during the peptide detection process so, even if a peptide is missing from one or more runs, its outline will still be found. This set of outlines is then applied to all aligned runs. If a peptide ion is absent from a particular run, an outline is placed were it would be. This means Progenesis LC-MS only measures a zero abundance if the peptide is truly missing.