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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 Other Files 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
B. burgdorferi 224326 Feb 2019 17 PSM FDR = 0.00005 3734760 39145 Bburgdorferi APD_BORBU_all.fasta prot_map chrom_map
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
C Elegans phospho 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
Zebrafish 7955 Mar 2014 29 PSM FDR = 0.004 2,543,623 108,273 Dr_CMP201403_ENS74_IPI3.87403+IPI 3.87+cRAP APD_Dr_all.fasta prot_map chrom_map MYSQL, XML
G. gallus 9031 Jul 2017 29 PSM FDR = 0.00008 5078871 109710 G. gallus APD_CHICK_all.fasta prot_map chrom_map
[ + ] 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
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 Jan 2021 2322 PSM FDR = 0.00015 437,319,124 2,520,734 THISP_2020-10-01 APD_Hs_all.fasta prot_map chrom_map MYSQL,TSV SampleType_Peptide_List.zip, Sample_Table.tsv
[ + ] 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
Human Heart 9606 Aug 2014 7 P >= 0.90 1,613,439 103,744 Ensembl v75.37+CompleteProteome_varsplic_PAB201406+IPI 3.87+cRAP 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 Dec 2016 157 PSM FDR = 0.00002 8,741,003 135,761 THISP_2016-10-01 APD_Hs_all.fasta prot_map chrom_map MYSQL, XML PhosphoPep-P0.95, PhosphoPep-All
[ + ] 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
[ + ] 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
[ + ] 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
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
[ + ] Mouse 10090 Jan 2016 117 PSM FDR = 0.0003 10438846 224625 Ensembl v78+UPSP+Trembl201506+IPI 3.87+cRAP+uniprotSNP APD_Mm_all.fasta prot_map chrom_map
[ + ] 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
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
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 2014 320 PSM FDR = 0.0012 4417907 87908 Pig_UPSP-var_RefSeq_201401_ENS74_nofrag APD_Pig_all.fasta prot_map chrom_map
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)
S. saureus COL 93062 Oct 2013 4 Prob = 0.9 255928 25373 S.Aureus_COL APD_STAAU_all.fasta prot_map chrom_map MYSQL
S. saureus HG001 93061 Seq 2014 15 PSM FDR = 0.005 1637033 75953 S.Aureus_HG001 APD_STAAU_all.fasta prot_map chrom_map MYSQL
[ + ] 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
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
Yeast (C. albicans) 237561 May 2014 20 PSM FDR = 0.01 838,646 61,642 CANAL_SC5314_version_A21_decoy APD_Canal_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