Table 1.

Total and non-redundant peptide spectra identified by N-terminal proteomics. N-terminal peptides corresponding to protease cleavage-sites as well as unblocked protein N-termini are sub-divided based on their proteolytic processing. Protein N-termini retaining the initiator Met are designated “Native N-terminus”, whereas those processed by Methionine Aminopeptidase are termed “Met removed”. Periplasmic secreted proteins that have been processed by signal peptidases are grouped as “Signal peptide removed”, and likewise proteins with annotated propeptide cleavages are shown as “Propeptide removed”. All other N-termini correspond to internal cleavage-sites that have not been annotated, and thus are termed “Unascribed cleavage”. Protease-of-interest cleavage-sites were found by sieving this last group for cleavage-sites found only in the protease treated samples and cleaved after an Asp for human caspase-3, or a Glu for GluC.

	human caspase-3		Staphylococcal GluC
Category	NR N-term	Spectra	NR N-term	Spectra
Native N-terminus	253	12,533	196	8,066
Met removed	209	9,991	148	7,448
Signal peptide removed	37	1,178	26	659
Propeptide removed	1	24	1	5
Unascribed cleavage	598	8,133	434	4,735
Total	1,098	31,859	805	20,913
Protease only	162	947	263	2,195
D or E in P1	57	490	100	767