Figure 15. Apportionment of shared peptides and creation of the protein-level summary list.

Peptides are apportioned among all their corresponding proteins, and a minimal list of proteins is derived that can explain all observed peptides. At the same time, peptide posterior probabilities are used to compute the protein probabilities. Proteins that are impossible to differentiate on the basis of identified peptides are presented as a group (G/E). It is not possible to conclude that protein B is present in the sample because it is identified by shared peptides only that can be explained by other proteins.