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PeptideAtlas Builds – Bulk Downloads

PeptideAtlas builds are performed for individual organisms and important sample groups (e.g., plasma/serum). The data products of these individual builds may accessed interactively in the database via the Stats & Lists page or with custom queries, or they may be downloaded in their entirety below.

Each build has a peptide inclusion cutoff criterion. A build with a cutoff of "P≥0.9" is a build in which only peptides with a PeptideProphet probability of at least 0.9 are included. A build with a PSM FDR (false discovery rate) threshold usually denotes a build with a protein FDR of 1%. For these builds, a peptide usually must have a probability much greater than 0.9 to be included.

For builds with P≥0.9 cutoffs, PSMs and peptides are counted only for multiply observed peptides; singletons are omitted because these identifications are quite unreliable at this generous cutoff.


Show Older Builds Build Name TaxID Date Number of Samples Peptide Inclusion Cutoff Number of Peptide-Spectrum Matches (PSMs) Number of Distinct Peptides Reference Database Peptide Sequences Peptide CDS Coordinates Peptide CDS and Chromosomal Coordinates Database Tables Spectral Library Comments
[+]
Honeybee 7460 Sep 2013 80 PSM FDR = 0.00004 4,102,541 35,074 amel_OGSv3.2 APD_Apis_all.fasta prot_map chrom_map MYSQL, XML splib
7460 Mar 2010 253 PSM FDR = 0.0007 1,339,806 27 Honeybee_Merge20090316_cRAP_plusNew APD_Apis_all.fasta prot_map chrom_map MYSQL, XML splib
Cow 9913 Dec 2011 109 PSM FDR = 0.00125 196791 8559 Ensembl Cow Protein Set v64 +,Swiss-Prot 2011-12 + other databases + cRAP + decoys APD_Bt_all.fasta prot_map chrom_map MYSQL, XML splib
[+]
C Elegans 6239 Sep 2013 34 PSM FDR = 0.0003 1,371,627 106,414 Ensembl C elegans Protein Set v67 + Uniprot2013-08 + wormbase 229 + crap + decoys APD_Ce_all.fasta prot_map chrom_map MYSQL, XML splib
6239 Aug 2011 25 PSM FDR = 0.002 823379 74554 Ensembl C elegans Protein Set v62 + Uniprot2011-08 + wormbase 215 + crap + decoys APD_Ce_all.fasta prot_map chrom_map MYSQL, XML splib
6239 May 2008 23 P>=0.9 767,040 52,594 Ensembl C.Elegans Protein Set 49-180a + Worm 170 APD_Ce_all.fasta prot_map chrom_map MYSQL, XML
C Elegans phoso 6239 June 2010 2 PSMFDR = 0.015 48067 7098 Ensembl C elegans Protein Set v57 + wormbase 215 + crap + decoys APD_Ce_all.fasta prot_map chrom_map MYSQL, XML
[+]
Drosophila 7227 Aug 2012 51 PSM FDR = 0.00001 332642 58746 UPSP_var_201207_Trembl_201205_ENS67 APD_Dm_all.fasta prot_map chrom_map MYSQL, XML
7227 Sep 2011 55 PSM FDR = 0.001 594956 53996 fgcz_7226_20050105_Ens62_uniprot-2011-08 APD_Dm_all.fasta prot_map chrom_map MYSQL, XML
7227 June 2010 53 PSM FDR = 0.001 391447 32234 fgcz_7227_20050105_Ens52_new APD_Dm_all.fasta prot_map chrom_map MYSQL, XML
7227 July 2009 51 PSM FDR =0.0008 367788 31184 fgcz_7227_20050105_Ens52 APD_Dm_all.fasta prot_map chrom_map MYSQL, XML
[+]
Halobacterium 64091 Aug 2013 95 PSM FDR = 0.001 282,691 16,163 Halobacterium Dataset 20080205 APD_Halo_all.fasta prot_map chrom_map MYSQL, XML
64091 Feb 2008 91 P>=0.9 121,618 14,730 Halobacterium GFF APD_Hbt_all.fasta prot_map chrom_map XML
64091 July 2006 88 P>=0.9 636,300 12,318 Halobacterium GFF APD_Hbt_all.fasta prot_map chrom_map XML published in Van et al. 2008
Horse 9796 Apr 2013 51 PSM FDR = 0.0008 534,093 24,131 Equus_caballus.fasta APD_MYG_all.fasta prot_map chrom_map MYSQL, XML
[+]
Human 9606 Aug 2013 515 PSM FDR = 0.0002 61,124,407 338,013 Ensembl Human Protein Set v67.37+ CompleteProteome_varsplic_PAB-_20121016 + cRAP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML splib
9606 Dec 2012 470 PSM FDR = 0.0002 43427557 253693 Ensembl Human Protein Set v67.37+CompleteProteome_varsplic_PAB-_20121016+cRAP APD_Hs_all.fasta prot_map chrom_map XML splib
9606 Jul 2012 467 PSM FDR = 0.0002 40450363 218799 Ensembl Human Protein Set v67.37+ IPI v3.71 + Swiss-Prot 201205+ cRAP + SNP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML splib
9606 Apr 2012 193 PSM FDR = 0.0003 12051573 144693 Ensembl Human Protein Set v64.37g+ IPI v3.71 + Swiss-Prot 201109+ cRAP + decoys APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 Nov 2011 337 PSM FDR = 0.0003 10299791 86441 Ensembl Human Protein Set v64.37g+ IPI v3.71 + Swiss-Prot 201110+ cRAP + decoys APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 May 2010 234 PSM FDR = 0.0003 5402374 56304 Ensembl Human Protein Set v57.37+ IPI v3.71 + Swiss-Prot 2010_04 + cRAP + decoys APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 Jun 2009 220 PSM FDR = 0.0001 2754771 38732 Ensembl + Swiss-Prot (incl. splice variants) + IPI
9606 Mar 2009 220 P >= 0.9 6683326 83931 Ensembl protein set 49 plus IPI 3.26 APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 Jul 2004 P >= 0.9 APD_Hs_all.fasta prot_map chrom_map published in Desiere et al. 2004
[+]
Human brain 9606 Aug 2013 23 P >= 0.9 620,813 29,292 Ensembl Human Protein Set v67.37+ CompleteProteome_varsplic_PAB-_20121016 + cRAP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML splib
9606 Sep 2012 19 PSM FDR = 0.0035 253253 15890 Ensembl Human Protein Set v67.37+ IPI v3.71 + Swiss-Prot 201205+ cRAP + SNP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 Dec 2011 19 PSM FDR = 0.0035 253253 15890 Ensembl Human Protein Set v64.37g+ IPI v3.71 + Swiss-Prot 201109+ cRAP + decoys APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 June 2011 19 PSM FDR = 0.0035 250515 13152 Ensembl Human Protein Set,v62.37g+ IPI v3.71 + Swiss-Prot 201105+ cRAP + decoys APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
Human kidney 9606 Aug 2013 13 P >= 0.9 938,113 38,989 Ensembl Human Protein Set v67.37+ CompleteProteome_varsplic_PAB-_20121016 + cRAP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML splib
Human liver 9606 Aug 2013 70 P >= 0.9 1,845,053 36,800 Ensembl Human Protein Set v67.37+ CompleteProteome_varsplic_PAB-_20121016 + cRAP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML splib
[+]
Human Phospho 9606 Oct 2013 35 PSM FDR = 0.0003 1,368821 35,100 Ensembl Human Protein Set v67.37+ CompleteProteome_varsplic_PAB-_20121016 + cRAP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 May 2013 27 PSM FDR = 0.0001 889,904 33,264 Ensembl Human Protein Set v67.37+ CompleteProteome_varsplic_PAB-_20121016 + cRAP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
[+]
Human plasma 9606 Aug 2013 127 PSM FDR = 0.0003 30,513,825 51,547 Ensembl Human Protein Set v67.37+ CompleteProteome_varsplic_PAB-_20121016 + cRAP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML splib
9606 Aug 2012 151 5E-05 27629049 49459 Ensembl Human Protein Set v67.37+ IPI v3.71 + Swiss-Prot 201205+ cRAP + SNP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML splib
9606 May 2010 91 no single PSM FDR cutoff or probability threshold for this build 3172689 20609 Ensembl Human Protein Set v57.37+ IPI v3.71 + Swiss-Prot 2010_04 + cRAP + decoys APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 Nov 2009 91 protein FDR 1.0% 3,176,380 20,709 Ensembl + Swiss-Prot (incl. splice variants) + IPI APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 Jul 2007 40 P >= 0.9 2,218,286 14,602 Ensembl 43.36e APD_Hs_all.fasta prot_map chrom_map MYSQL, XML special publication build
9606 Mar 2005 P >= 0.9 APD_Hs_all.fasta prot_map chrom_map Published in Deutsch et al. 2005
[+]
Human urine 9606 Aug 2013 15 P >= 0.9 425,579 23,739 Ensembl Human Protein Set v67.37+ CompleteProteome_varsplic_PAB-_20121016 + cRAP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML splib
9606 Sep 2012 6 PSM FDR = 0.003 37064 6458 Ensembl Human Protein Set v67.37+ IPI v3.71 + Swiss-Prot 201205+ cRAP + SNP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
9606 June 2010 6 PSM FDR = 0.003 37064 6458 Ensembl Human Protein Set v57.37+ IPI v3.71 + Swiss-Prot 2010_04 + cRAP + decoys APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
[+]
Human Others 9606 Aug 2013 336 PSM FDR = 0.0002 29,592,772 318,317 Ensembl Human Protein Set v67.37+ CompleteProteome_varsplic_PAB-_20121016 + cRAP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML splib
9606 Aug 2012 299 0.0003 12628823 201597 Ensembl Human Protein Set v67.37+ IPI v3.71 + Swiss-Prot 201205+ cRAP + SNP APD_Hs_all.fasta prot_map chrom_map MYSQL, XML
Human Glyco Synthetic Peptides 9606 Jul 2012 3 P>=0.9 109602 4220 Hs_SP_v2011-08_TargDecoy APD_Hs_all.fasta prot_map chrom_map splib Huttenhain, et al. (2013)
[+]
Leptospira interrogans 173 Aug 2013 8 PSM FDR = 0.007 248,430 29,137 LInterrogans_200802_build APD_Li_all.fasta prot_map chrom_map MYSQL, XML splib
173 Jan 2008 6 P>=0.9 145703 18303 LInterrogans_200802_build APD_Li_all.fasta prot_map chrom_map MYSQL, XML
[+]
Mouse 10090 Jun 2013 92 PSM FDR = 0.00025 4001770 101695 Ensembl MouseProtein Set v67.37+ IPI v3.72 + Swiss-Prot 201205+ cRAP APD_Mm_all.fasta prot_map chrom_map MYSQL, XML
10090 Feb 2013 91 PSM FDR = 0.00025 4,001,770 101,695 Ensembl MouseProtein Set v67.37+ IPI v3.72 + Swiss-Prot 201205+ cRAP APD_Mm_all.fasta prot_map chrom_map splib
10090 Sep 2012 88 PSM FDR = 0.00025 2320012 37494 Ensembl MouseProtein Set v67.37+ IPI v3.72 + Swiss-Prot 201205+ cRAP APD_Mm_all.fasta prot_map chrom_map MYSQL, XML splib
10090 Dec 2011 88 PSM FDR = 0.00025 2320012 37494 Ensembl Mouse Protein Set v64.37 + IPI v3.72 + Swiss-Prot 201109 + cRAP + decoys APD_Mm_all.fasta prot_map chrom_map MYSQL, XML
10090 June 2011 88 PSM FDR = 0.0003 2312703 30261 Ensembl Mouse Protein Set v37.62 + IPI v3.72 + Swiss-Prot 2011-05 + cRAP + decoys APD_Mm_all.fasta prot_map chrom_map MYSQL, XML
10090 June 2010 84 PSM FDR = 0.001% 1815096 38574 Ensembl Mouse Protein Set v37.57 + IPI v3.72 + Swiss-Prot 2010_04 + cRAP + decoys APD_Mm_all.fasta prot_map chrom_map MYSQL, XML
10090 Aug 2009 68 PSM FDR = 0.0000075% 576,448 12764 Ensembl + Swiss-Prot (incl. splice variants) + IPI APD_Mm_all.fasta prot_map chrom_map MYSQL, XML
[+]
Mouse Plasma 10090 Sep 2012 20 PSM FDR = 0.00006 889380 7665 Ensembl MouseProtein Set v67.37+ IPI v3.72 + Swiss-Prot 201205+ cRAP APD_Mm_all.fasta prot_map chrom_map MYSQL, XML
10090 Dec 2011 20 PSM FDR = 0.00006 889380 7665 Ensembl Mouse Protein Set v64.37 + IPI v3.72 + Swiss-Prot 201109 + cRAP + decoys APD_Mm_all.fasta prot_map chrom_map MYSQL, XML
10090 Sep 2011 20 PSM FDR = 0.00006 888280 6565 Ensembl Mouse Protein Set v37.62 + IPI v3.72 + Swiss-Prot 2011-05 + cRAP + decoys APD_Mm_all.fasta prot_map chrom_map MYSQL, XML
10090 June 2010 19 PSM FDR = 0.0001 757887 5946 Ensembl Mouse Protein Set v37.57 + IPI v3.72 + Swiss-Prot 2010_04 + cRAP + decoys APD_Mm_all.fasta prot_map chrom_map MYSQL, XML
Mouse Glyco Synthetic Peptides 10090 Jul 2012 3 P>=0.9 67346 2339 Mm_SP_v2011-08_TargDecoy APD_Mm_all.fasta prot_map chrom_map splib Huttenhain, et al. (2013)
[+]
Mtuberculosis 1773 July 2013 12 PSM FDR = 0.001 1,134,715 50,288 TubercuList-R27 APD_MTB_all.fasta prot_map chrom_map MYSQL, XML splib
1773 Mar 2013 4 PSM FDR = 0.0025 884562 48476 TubercuList_v2-3_Crap_Decoy APD_MTB_all.fasta prot_map chrom_map splib Schubert, et al. (2013)
1773 Feb 2012 8 PSM FDR = 0.002 884562 48476 TubercuList_v2-3_Crap_Decoy APD_MTB_all.fasta prot_map chrom_map MYSQL, XML
1773 Sep 2011 2 PSM FDR = 0.0025 650426 28236 TubercuList_v2-3_Decoy APD_MTB_all.fasta prot_map chrom_map MYSQL, XML
Mtuberculosis Synthetic Peptides 1773 Mar 2013 4 no single PSM FDR cutoff or probability threshold for this build 16578 3873 TubercuList_v2-3_Crap_Decoy APD_MTB_all.fasta prot_map chrom_map splib Schubert, et al. (2013)
Pfalciparum 5833 Sep 2012 2 PSM FDR = 0.00005 186,215 14,494 P.falciparum_v9.1_decoy APD_Pf_all.fasta prot_map chrom_map MYSQL, XML Lindner et al. (2013)
Pyoelii 73239 Sep 2012 2 PSM FDR = 0.00005 120,684 10,140 P.yoelii_v9.1_decoy APD_Py_all.fasta prot_map chrom_map MYSQL, XML Lindner et al. (2013)
Pig 9823 Nov 2011 292 PSM FDR = 0.0002 1511129 13883 Ensembl Pig Protein Set v62 + Swiss-Prot, 2011-08 + cRAP + decoys APD_Pig_all.fasta prot_map chrom_map MYSQL, XML splib
Rat 10116 Nov 2013 20 PSM FDR = 0.0025 2,926,833 288 RAT ENS67, IPI 3.87, Complete Proteome 201310 APD_Rn_all.fasta prot_map chrom_map MYSQL, XML splib Low et al. (2013)
[+]
Yeast 4932 Mar 2013 90 PSM FDR = 0.0001 3,179,070 86,836 Ens67_uniprot_201202_S288C_crap APD_Sc_all.fasta prot_map chrom_map MYSQL, XML
4932 Dec 2011 63 PSM FDR = 1E-04 2880633 60313 Ensembl Sc_v64_3 + SGD_S288C+ Swiss-Prot 201110 + cRAP + decoys APD_Sc_all.fasta prot_map chrom_map MYSQL, XML
4932 Apr 2009 60 P>=0.9 2512202 60720 Yeast Combined Nonredundant sequences 2007-02-07 forward and decoy APD_Sc_all.fasta prot_map chrom_map MYSQL, XML
Yeast MRM 4932 Feb 2008 1 P>=0.9 31484 5078 Yeast Combined Nonredundant sequences 2007-02-07 forward and decoy APD_Sc_all.fasta prot_map chrom_map MYSQL, XML
Fisson Yeast 4896 Aug 2012 1 PSM FDR = 0.00005 1194156 49311 pompep_100324 APD_SPOM_all.fasta prot_map chrom_map splib Gunaratne et al. (2013)
Streptococcus 1314 Feb 2007 5 P>=0.9 48174 5360 Streptococcus pyogenes protein list APD_Sp_all.fasta prot_map chrom_map MYSQL, XML

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