129	datasets
365	experiments
19,852	MS runs
406,364,454	spectra searched
44,895,051	PSMs
264,244	distinct phosphopeptides
9,810	canonical proteins

About

The Human Phospho PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry proteomics datasets.

Available Human Phospho datasets were reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools.

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All detected Human Phospho proteins

Chromosome Summary

Chromosome	neXtProt entries	Canonical		Uncertain		Redundant		Not Observed
1	2,065	1,049	50.8%	275	13.3%	107	5.2%	634	30.7%
2	1,295	658	50.8%	219	16.9%	78	6.0%	340	26.3%
3	1,076	549	51.0%	156	14.5%	37	3.4%	334	31.0%
4	766	348	45.4%	110	14.4%	32	4.2%	276	36.0%
5	887	432	48.7%	135	15.2%	61	6.9%	259	29.2%
6	1,029	495	48.1%	161	15.6%	46	4.5%	327	31.8%
7	1,029	448	43.5%	130	12.6%	70	6.8%	381	37.0%
8	706	355	50.3%	99	14.0%	16	2.3%	236	33.4%
9	806	385	47.8%	116	14.4%	31	3.8%	274	34.0%
10	748	393	52.5%	109	14.6%	31	4.1%	215	28.7%
11	1,333	577	43.3%	160	12.0%	42	3.2%	554	41.6%
12	1,035	532	51.4%	160	15.5%	42	4.1%	301	29.1%
13	333	171	51.4%	48	14.4%	8	2.4%	106	31.8%
14	736	320	43.5%	93	12.6%	21	2.9%	302	41.0%
15	609	319	52.4%	96	15.8%	26	4.3%	168	27.6%
16	843	440	52.2%	122	14.5%	46	5.5%	235	27.9%
17	1,170	596	50.9%	160	13.7%	44	3.8%	370	31.6%
18	270	155	57.4%	33	12.2%	11	4.1%	71	26.3%
19	1,437	623	43.4%	227	15.8%	207	14.4%	380	26.4%
20	550	272	49.5%	76	13.8%	17	3.1%	185	33.6%
21	247	96	38.9%	27	10.9%	8	3.2%	116	47.0%
22	506	218	43.1%	70	13.8%	32	6.3%	186	36.8%
X	850	370	43.5%	148	17.4%	67	7.9%	265	31.2%
Y	48	5	10.4%	4	8.3%	20	41.7%	19	39.6%
MT	15	1	6.7%	1	6.7%	0	0.0%	13	86.7%
?	6	1	16.7%	0	0.0%	0	0.0%	5	83.3%

PE	neXtProt entries	Canonical		Uncertain		Redundant		Not Observed
1	18,397	9,791	53.2%	2,877	15.6%	875	4.8%	4,854	26.4%
2	1,188	0	0.0%	31	2.6%	128	10.8%	1,029	86.6%
3	180	0	0.0%	0	0.0%	6	3.3%	174	96.7%
4	13	0	0.0%	0	0.0%	1	7.7%	12	92.3%
5	611	12	2.0%	27	4.4%	90	14.7%	482	78.9%
1-4	19,778	9,791	49.5%	2,908	14.7%	1,010	5.1%	6,069	30.7%
2022-04 Total	20,389	9,803	48.1%	2,935	14.4%	1,100	5.4%	6,551	32.1%

Chromosome	All (PE 1-5)	PE1	PE2	PE3	PE4	PE5	PE1-4
1	2,065	1,864	124	28	2	47	2,018
2	1,295	1,229	47	1	0	18	1,277
3	1,076	1,006	45	6	0	19	1,057
4	766	707	27	12	0	20	746
5	887	838	34	2	0	13	874
6	1,029	938	53	3	1	34	995
7	1,029	878	93	5	2	51	978
8	706	627	34	9	0	36	670
9	806	703	57	2	2	42	764
10	748	690	39	0	1	18	730
11	1,333	1,072	159	61	0	41	1,292
12	1,035	962	40	8	0	25	1,010
13	333	310	10	2	0	11	322
14	736	648	59	14	2	13	723
15	609	534	41	3	0	31	578
16	843	775	42	0	1	25	818
17	1,170	1,080	60	4	0	26	1,144
18	270	255	5	0	0	10	260
19	1,437	1,318	79	10	1	29	1,408
20	550	509	24	1	0	16	534
21	247	198	22	4	0	23	224
22	506	454	25	3	1	23	483
X	850	758	57	2	0	33	817
Y	48	33	8	0	0	7	41
MT	15	15	0	0	0	0	15
?	6	2	4	0	0	0	6

Column descriptions ▲

Entries: Number of entries in each chromosome
Canonical: Proteins seen with 2 distinct, uniquely mapping peptides
Uncertain: Proteins with some evidence that is not sufficient for canonical status
Redundant: Proteins that have peptides that map to them, but not uniquely and thus not needed to explain the observed peptides
Not Observed: No detections at all in PeptideAtlas above our very stringent threshold

Publications

A publication describing the Human Phospho PeptideAtlas build is in progress. For now, please just reference this URL, and check back later for a citation.

Download

Below are individual Human Phospho PeptideAtlas builds available for download in various flat file formats. Note that not all files contain all information from the build. A build subtitled "PSM FDR=0.002" denotes a PSM FDR threshold of 0.002 (0.2%) is applied to every sample in the build.

Human Phospho 2022-04 PSM FDR = 0.0001Latest Build

Biosequence Set in FASTA format [598MB]
Peptide CDS and chromosomal coordinates [439MB]
Peptide CDS coordinates [251MB]
Peptide sequences in FASTA format [8MB]

Human Phospho 2021-01 PSM FDR = 0.0002

Biosequence Set in FASTA format [511MB]
Peptide CDS and chromosomal coordinates [335MB]
Peptide CDS coordinates [189MB]
Peptide sequences in FASTA format [6MB]

Human Phospho 2016-12 PSM FDR = 0.00002

Biosequence Set in FASTA format [3GB]
Database tables exported as an XML file [320MB]
Database tables exported as mysql dump file [239MB]
Peptide CDS and chromosomal coordinates [177MB]
Peptide CDS coordinates [98MB]
Peptide sequences in FASTA format [4MB]

Human Phospho 2013-10 PSM FDR = 0.0003

Biosequence Set in FASTA format [278MB]
Database tables exported as an XML file [39MB]
Database tables exported as mysql dump file [23MB]
Peptide CDS and chromosomal coordinates [33MB]
Peptide CDS coordinates [16MB]
Peptide sequences in FASTA format [1MB]

Human Phospho 2013-05 PSM FDR = 0.0001

Biosequence Set in FASTA format [278MB]
Database tables exported as an XML file [38MB]
Database tables exported as mysql dump file [22MB]
Peptide CDS and chromosomal coordinates [31MB]
Peptide CDS coordinates [15MB]
Peptide sequences in FASTA format [984KB]

Help

Complete description of each of the available download formats

Other Resources

Acknowledgements

We gratefully acknowledge the support for the Human Phospho PeptideAtlas from NSF grant 1933311 “PTMexchange: Globally harmonized re-analysis and sharing of data on post-translational modifications”.