Figure 1

Classification of proteins into four evidence groups. 9 different proteins (Protein A to Protein I) comprising 6 different peptides (boxes 1 to 6) have been used to illustrate all possible scenarios. Conclusive proteins have at least one unique peptide; indistinguishable proteins have the same peptides including at least one discriminating peptide; ambiguous group is formed by proteins sharing discriminating peptides; non-conclusive proteins only have non-discriminating peptides.