Table 1. Performance evaluation of the linear SVMs across five PTM types. The number of true positive sites used in the 10-fold cross-validation is about half the amount of data present in the PSP database after removal of redundant protein sequences and those that do not have secondary structure information from SPIDER3. AUC – area-under-the-curve; MCC – the highest Matthew's correlation coefficient at all score thresholds; sensitivity/specificity at score threshold corresponding to the highest MCC value.

PTM type	No. of proteins	No. of PSP sites	Window size 25
			AUC	MCC	Sensitivity	Specificity
Acetylation (K)	3729	10 479	0.66	0.25	0.61	0.64
Methylation (K)	1521	2566	0.74	0.39	0.61	0.76
Ubiquitination (K)	4874	22 592	0.64	0.22	0.67	0.54
SUMOylation (K)	1020	2996	0.77	0.42	0.63	0.79
Methylation (R)	2301	5450	0.79	0.47	0.62	0.84
Phosphorylation (S)	8510	76 008	0.74	0.36	0.70	0.66
Phosphorylation (T)	6982	28 359	0.72	0.33	0.66	0.66
Phosphorylation (Y)	6097	18 645	0.70	0.30	0.72	0.58