33	datasets
63	experiments
1,302	MS runs
10,514,318	PSMs
181,045	distinct peptides
4,985	canonical proteins

About

The Human Plasma / Extracellular Vesicles PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry proteomics datasets.

Available Human Plasma / Extracellular Vesicles datasets were reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools.

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4,985 canonical proteins

Chromosome Summary

Chromosome	neXtProt entries	Canonical		Uncertain		Redundant		Not Observed
1	2,065	542	26.2%	204	9.9%	252	12.2%	1,067	51.7%
2	1,295	383	29.6%	133	10.3%	142	11.0%	637	49.2%
3	1,076	286	26.6%	122	11.3%	107	9.9%	561	52.1%
4	766	168	21.9%	85	11.1%	119	15.5%	394	51.4%
5	887	215	24.2%	96	10.8%	102	11.5%	474	53.4%
6	1,029	247	24.0%	120	11.7%	129	12.5%	533	51.8%
7	1,029	200	19.4%	116	11.3%	124	12.1%	589	57.2%
8	706	157	22.2%	79	11.2%	71	10.1%	399	56.5%
9	806	192	23.8%	89	11.0%	85	10.5%	440	54.6%
10	748	185	24.7%	89	11.9%	98	13.1%	376	50.3%
11	1,333	301	22.6%	124	9.3%	142	10.7%	766	57.5%
12	1,035	265	25.6%	121	11.7%	110	10.6%	539	52.1%
13	333	75	22.5%	40	12.0%	51	15.3%	167	50.2%
14	736	224	30.4%	73	9.9%	70	9.5%	369	50.1%
15	609	144	23.6%	57	9.4%	69	11.3%	339	55.7%
16	843	197	23.4%	103	12.2%	104	12.3%	439	52.1%
17	1,170	314	26.8%	115	9.8%	138	11.8%	603	51.5%
18	270	65	24.1%	33	12.2%	44	16.3%	128	47.4%
19	1,437	329	22.9%	283	19.7%	162	11.3%	663	46.1%
20	550	135	24.5%	47	8.5%	68	12.4%	300	54.5%
21	247	39	15.8%	27	10.9%	18	7.3%	163	66.0%
22	506	158	31.2%	56	11.1%	66	13.0%	226	44.7%
X	850	163	19.2%	76	8.9%	81	9.5%	530	62.4%
Y	48	1	2.1%	8	16.7%	7	14.6%	32	66.7%
MT	15	4	26.7%	4	26.7%	1	6.7%	6	40.0%
?	6	0	0.0%	0	0.0%	0	0.0%	6	100.0%

PE	neXtProt entries	Canonical		Uncertain		Redundant		Not Observed
1	18,397	4,980	27.1%	2,244	12.2%	2,190	11.9%	8,983	48.8%
2	1,151	3	0.3%	40	3.5%	90	7.8%	1,018	88.4%
3	215	0	0.0%	2	0.9%	11	5.1%	202	94.0%
4	15	0	0.0%	0	0.0%	1	6.7%	14	93.3%
5	611	2	0.3%	13	2.1%	68	11.1%	528	86.4%
1-4	19,778	4,983	25.2%	2,286	11.6%	2,292	11.6%	10,217	51.7%
2023-04 Total	20,389	4,985	24.4%	2,299	11.3%	2,360	11.6%	10,745	52.7%

Chromosome	All (PE 1-5)	PE1	PE2	PE3	PE4	PE5	PE1-4
1	2,065	1,864	117	35	2	47	2,018
2	1,295	1,229	45	3	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	52	4	1	34	995
7	1,029	878	90	7	3	51	978
8	706	627	32	10	1	36	670
9	806	703	51	8	2	42	764
10	748	690	38	1	1	18	730
11	1,333	1,072	151	69	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	58	15	2	13	723
15	609	534	41	3	0	31	578
16	843	775	40	2	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	77	12	1	29	1,408
20	550	509	24	1	0	16	534
21	247	198	22	4	0	23	224
22	506	454	24	4	1	23	483
X	850	758	57	2	0	33	817
Y	48	33	7	1	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

If you use the Human Plasma / Extracellular Vesicles PeptideAtlas builds for your work, please cite:

Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM, Advances and Utility of the Human Plasma Proteome, J Proteome Res. 2021 Dec 3;20(12):5241-5263

Download

Below are individual Human Plasma / Extracellular Vesicles 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 Plasma EV 2024-04 PSM FDR = 0.001Latest Build

Biosequence Set in FASTA format [700MB]
Peptide CDS and chromosomal coordinates [407MB]
Peptide CDS coordinates [243MB]
Peptide sequences in FASTA format [5MB]

Human Plasma EV 2021-06 PSM FDR = 0.001

Biosequence Set in FASTA format [511MB]
Database tables exported as mysql dump file [65MB]
Peptide CDS and chromosomal coordinates [181MB]
Peptide CDS coordinates [105MB]
Peptide sequences in FASTA format [2MB]

Help

Complete description of each of the available download formats

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