Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources

Table 2 Databases of phosphorylation sites

Name	Last update	Method of access	Version	Sites	Proteins	Kinases	Phosphatases	Data Type	References
PhosphoPep	2007	Web\|DL	2.0	3980				MS	[30, 31]
HPRD	2010	Web\|DL	9	78,005	11,807	291	42	UNSP	[21, 107, 108]
Phospho.ELM	2010	Web\|DL	9.0	26,651	5374	250		HT, LT	[24, 109, 110]
Phospho3D	2010	Web\|DL	2.0	1770		59		HT, LT	[44]
PHOSIDA	2011	Web\|DL	3.24	24,262	8283			MS	[26, 111]
HuPho	2012	Web\|DL		190	121		55	UNSP	[18]
PTMfunc	2012	Web		31,165				MS	[32]
ANIA	2013	Web\|DL		305	220			LT	[35, 112]
PhosphoNetworks	2013	Web\|DL			1140	255		UNSP	[36]
RegPhos	2013	Web\|DL	2.0	66,301	10,849	380		UNSP	[42, 113]
Kinome NetworkX	2014	DL		173,460	18,610	357		UNSP	[41]
ProteomeScout	2014	Web\|DL	2	290,007	23,387			MS	[39, 114]
LymPHOS	2015	Web\|DL	2	15,566	4937			MS	[27, 115]
PhosphoDB	2015	Web		25,864	6222			MS	[29]
dbPAF	2016	Web\|DL	1.0	244,034	18,773			UNSP	[38]
DEPOD	2016	Web\|DL	1.1	253	210		88	UNSP	[19]
KANPHOS	2016	Web	β			73		MS	[25]
PhosphoAtlas	2016	DL		2595	1284	501		UNSP	[1]
Phosphopedia	2016	Web	1.0	109,611	11,428			MS	[28]
Phosphatome	2017	Web	3	6008	2000	319	106	UNSP	[20]
PhosphoNET	2017	Web		966,817^a	22,698	488		UNSP + pred	[43]
PTMD	2018	Web\|DL	1.0	690	434			UNSP	[37]
qPhos	2018	Web\|DL		199,071	18,402			MS	[33]
dbPTM	2019	Web\|DL	v2019	257,527	19,713	25		UNSP	[40, 64, 116, 117]
PhosphoSitePlus	2019	Web\|DL	Aug-19	239,664	20,115	372		HT, LT	[23]
Signor	2019	Web\|DL	May-19	3593	1285	336	70	UNSP	[34, 118]
Swiss-Prot	2019	Web\|DL	Jun-19	40,135	7965	352		UNSP	[22, 119]

The number of unique kinases and phosphatases reported to phosphorylate sites in the database is included. For some databases, these numbers include enzyme groups in addition to individual enzymes. Data type indicates whether the data are from mass spectrometry (MS) experiments, separated high-throughput (HT) and low-throughput (LT) experiments, or whether the database combines data from both HT and LT experiments without specifying (UNSP)
^aIndicates inclusion of predicted phosphorylation sites (pred)