Table II. Classification of phosphorylation sites according to matched ions assigned by PhosCalc version 1.2.

Phosphorylation sites that had at least one more matched ion than any other potential site were classified as unambiguous. Ambiguous class I sites are indeterminable and have more than one with equal numbers of matched ions. The remaining phosphorylation sites that had fewer matched ions than at least one other site were classified as ambiguous class II.

Species	Class	Sites	Ser	Thr	Tyr
Soybean	Unambiguous	534	408 (76.4%)	79 (14.8%)	47 (8.8%)
	Ambiguous class I	281	183 (65.1%)	68 (24.2%)	30 (10.7%)
	Ambiguous class II	380	234 (61.6%)	90 (23.7%)	56 (14.7%)
Rapeseed	Unambiguous	320	234 (73.1%)	49 (15.3%)	37 (11.6%)
	Ambiguous class I	186	103 (55.4%)	62 (33.3%)	21 (11.3%)
	Ambiguous class II	312	147 (47.1%)	107 (34.3%)	58 (18.6%)
Arabidopsis	Unambiguous	172	145 (84.3%)	19 (11.0%)	8 (4.7%)
	Ambiguous class I	78	46 (59.0%)	20 (25.6%)	12 (15.4%)
	Ambiguous class II	151	83 (55.0%)	49 (32.5%)	19 (12.6%)