Figure 5.

Illustration of the two-step strategy for whole-cell protein identification. The initial step (Step 2 in Figure 2) involves the classification of top-ranking peptides from each protein identification tool into unique and non-unique peptide pools, which are subsequently used for protein identification. The last step (Step 5 in Figure 2) cross-compares the identified proteins from previous step: common proteins identified in the cross-comparison step are more confident than the non-common ones.