Table 1. Categorizing Serine (Ser), Threonine (Thr), and Tyrosine (Tyr) Sites from UniProt’s Reference Human Proteome into Phosphorylation Likelihood Sets Based on Available Phosphorylation Evidence in PhosphoSitePlus (PSP) and PeptideAtlas (PA).

Phosphorylation likelihood set	Phosphorylation evidence per site	Ser count	Thr count	Tyr count
High in PSP	5+ pieces of evidence	32 306	8161	9763
Medium in PSP	2–4 pieces of evidence	34 154	12 197	7228
Low in PSP	1 piece of evidence	66 777	35 173	20 191
High in PA	5+ observations at PTM score >0.95 which is ≥10% of total observations	26 186	4204	1169
Medium in PA	5+ observations at PTM score >0.95 which is <10% of total observations OR 2–4 observations at PTM score >0.95	20 517	5297	1460
Low in PA	1 observation at PTM score >0.95	12 950	4895	1324
Not phosphorylated	0 observations at PTM score >0.19 AND 5+ observations at PTM score ≤0.19 AND no evidence in PSP	13 892	8462	2184
Other sites	At least 1 observation in PA but does not fall into any other PA categories AND no evidence in PSP	60 221	35 000	10 009