Fig. 3.

Schematic example of the process of selecting peptides to represent protein abundance, for heavy and light labelling states (peptides are split into two groups according to their attributed labelling states). Green boxes represent that a given peptide was detected in a given fraction. A) Scenario A. The peptide present in the highest number of fractions within each labelling state is considered the representative peptide (in this example Peptide 2 for heavy and Peptide 1 for light). Thus, for the same protein, the peptide picked for one labelling state may be different from the peptide selected for the other. This scenario picks a representative peptide for all proteins, even if they are present only in one labelling state. B) Scenario B. The selected representative peptide is the one that is present in the highest number of fractions, for both labelling states considered together. Thus, for the same protein, the representative peptide selected is the same for both labelling states. In this scenario a representative peptide cannot be selected for proteins that do not have shared peptides or are not present in both labelling states. The peptide present in both samples and in the highest number of fractions (column H + L) is selected as representative (Peptide 2).