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:

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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