Table 2.

True positive rate at mass tolerance of 0.04 Da.

Type of methylation	True positive rate (%)	No. of methylation sites correctly matched	No. of methylation sites tested	No. of peptides tested
a) Non-redundant known mono- and di-methylation
Monomethyl-K	100	27	466	1,201
Dimethyl-K	98	89	280	699
Monomethyl-R	N.D.a	N.D.a	3	6
Dimeth-R	76	28	137	495
b) Artificial mono- and di-methylation
Monomethyl-K	78	217	11,377	30,782
Dimethyl-K	89	3,673	11,377	30,691
Monomethyl-R	90	453	6,941	18,728
Dimethyl-R	90	2,140	6,902	18,594

a: N.D. - not determined