Table 4.

Frequency of matching different ion types in ETD spectra of peptides produced by different cleavages. Numbers represent the fraction of all matched peaks in a given spectrum that match to each ion type. Results are separated into those from doubly-charged precursor ions and those of a higher charge state. (Note: tryptic numbers differ slightly from Table 3 due to the lack of consideration of ‘x’ ions).

Enzyme Prec. Charge	LysC 2+	LysC >2+	LysN 2+	LysN >2+	CNBr 2+	CNBr >2+	Trypsin 2+	Trypsin >2+
b	0.02	0.03	0.06	0.04	0.04	0.05	0.03	0.03
c-1	0.11	0.05	0.17	0.06	0.14	0.08	0.10	0.04
c	0.20	0.33	0.49	0.42	0.31	0.36	0.11	0.34
y	0.13	0.09	0.05	0.06	0.06	0.06	0.14	0.11
z	0.30	0.29	0.17	0.27	0.27	0.25	0.31	0.31
z+1	0.23	0.20	0.07	0.15	0.18	0.21	0.32	0.17