Figure 5.

Example of terminal peptide and cleavage site identification by semi-specific searches

In standard shotgun proteomics, only peptides whose N- and C-termini are both in accordance with the specificity of the used enzyme are considered. The N terminus of native protein N-terminal peptide (highlighted in green) does not match to the specificity of LysargiNase (cleavage at N-terminal side of K/R, highlighted in blue), but can be identified in the conventional LysargiNase-specific search. In N-terminal free semi-specific search, peptides whose N terminus does not match the specificity of LysargiNase (highlighted in red) can be additionally identified. Similarly, the C terminus of native protein C-terminal peptide (highlighted in green) does not match the specificity of trypsin/LysC (trypsin/P; cleavage at the C-terminal side of K/R, highlighted in blue), but can be identified in the conventional trypsin/P-specific search. In C-terminal free semi-specific search, peptides whose C terminus does not match the specificity of trypsin/LysC (highlighted in red) can be additionally identified.