Four external biological databases related to protein post-translational modification information, Swiss-Prot, Phospho.ELM, O-GLYCBASE, and UbiProt, are integrated into the proposed resource. As shown in bellow table, release 53.0 of Swiss-Prot contributes 17,957 experimental validated PTM sites within 8,086 proteins, and 124,933 putative PTM sites (annotated as "by similarity", "potential" or "probable" in the 'MOD_RES' fields) within 29,356 proteins. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues are known to be phosphorylated by cellular kinases. 13,612 experimentally verified phosphorylation sites within 4,419 proteins were obtained from Phospho.ELM version 6.0. O-GLYCBASE version 6.0 provides 242 glycoproteins containing 2,765 experimentally verified O-linked, N-linked, and C-linked glycosylation sites. However, 185 glycoproteins in O-GLYCBASE are corresponded to Swiss-Prot proteins, which have 2,353 experimentally verified glycosylation sites. Especially, a novel PTM database, UbiProt, stores 417 ubiquitylated proteins which contain 165 ubiquitylation sites.

The statistics of the experimental and putative PTM sites from dbPTM 2.0 were shown in Table 1. The collected PTM sites from Swiss-Prot, Phospho.ELM, O-GLYCBASE and UbiProt were categorized by the PTM type, after removing the redundancy, the number of non-redundant sites in each type of PTM were calculated. There were totally 36,466 experimentally verified PTM sites in dbPTM 2.0; therein, the type with maximum number of experimental sites is phosphorylation, consisting of 22,363 sites. To provide more potential PTM information to proteins without PTM annotations, 20 types of PTM sites were fully predicted against Swiss-Prot protein sequences by the learned HMMs with the threshold of specificity 100%, predicted totally 2,860,047 sites. With various types of kinase, especially, phosphorylation contains the maximum number of predicted sites.