is a Data Source.
PeptideAtlas, from the Institute for Systems Biology (ISB), is a compendium of peptides identified in tandem mass spectrometry proteomics experiments. Raw data from public datasets are reprocessed through a uniform pipeline (the Trans-Proteomic Pipeline) and mapped to reference proteomes and genomes, producing organism- and sample-specific builds. On 2026-10-04 its build index listed 110 builds across 39 organism groups, including the Human 2026-01 build. The project also runs PASSEL, a repository for SRM experiments, and SRMAtlas, a library of targeted proteomics assays.
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Eric W. Deutsch
ORCID: 0000-0001-8732-0928
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| peptideatlas.portal | PeptideAtlas Portal | peptideatlas.org | Graphical Interface | http | PeptideAtlas web portal for browsing ... |
| peptideatlas.builds | PeptideAtlas Build Index | main.cgi?output_format=json | Product | json | Machine-readable JSON index of all Pe... |
| peptideatlas.human.peptides | PeptideAtlas Human Peptides FASTA | APD_Hs_all.fasta (160.0 MB) | Product | fasta | FASTA file of all distinct peptides o... |
| peptideatlas.human.tables | PeptideAtlas Human Build Tables | atlas_build_607.tsv.zip (6.3 GB) | Product | tsv | Tab-separated tables of the Human 202... |
| peptideatlas.human.mysql | PeptideAtlas Human Build MySQL Dump | atlas_build_607.mysql.gz (5.4 GB) | Product | mysql | MySQL dump of the Human 2026-01 Pepti... |
| peptideatlas.human.ensembl-mapping | PeptideAtlas Human Peptide to Ensembl Mapping | APD_ensembl_hits.tsv (10.9 GB) | Mapping | tsv | Mapping of Human 2026-01 PeptideAtlas... |
| peptideatlas.human.coordinates | PeptideAtlas Human Peptide Coordinates | coordinate_mapping.txt (17.7 GB) | Product | txt | Genome coordinate mapping of peptides... |
| peptideatlas.search | PeptideAtlas Peptide Search | GetPeptides | Graphical Interface | http | SBEAMS search interface for querying ... |
| peptideatlas.repository | PeptideAtlas Data Repository | repository | Graphical Interface | http | PeptideAtlas data repository, which h... |
| peptideatlas.passel | PASSEL | passel | Graphical Interface | http | PASSEL (PeptideAtlas SRM Experiment L... |
| peptideatlas.srmatlas | SRMAtlas | srmatlas.org | Graphical Interface | http | SRMAtlas, a compendium of targeted pr... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| omicsdi.portal | OmicsDI Portal | www.omicsdi.org | Graphical Interface | http | had primary source | Web portal for searching and browsing... |
| omicsdi.api | OmicsDI API | index.html | Programming Interface | http | had primary source | Swagger-documented web service for pr... |
| proteomexchange.proteomecentral | ProteomeCentral | proteomecentral.proteomexchange.org | Graphical Interface | http | had primary source | ProteomeCentral, the central index of... |
| proteomexchange.dataset-list | ProteomeXchange Dataset Listing | GetDataset?outputMode=tsv | Product | tsv | had primary source | Full tab-separated listing of all pub... |
| proteomexchange.dataset-records | ProteomeXchange Dataset Records | GetDataset?ID=PXD000001&outputMode=XML | Product | xml | had primary source | Per-dataset ProteomeXchange announcem... |
PeptideAtlas is a multi-organism compendium of peptides identified in tandem mass spectrometry (MS/MS) proteomics experiments, run by the Institute for Systems Biology (ISB) in Seattle. Public datasets, many of them deposited through ProteomeXchange repositories, are reprocessed with the Trans-Proteomic Pipeline (Comet, X!Tandem, SpectraST, PeptideProphet, ProteinProphet). Identified peptides are mapped to reference protein sequences and genome coordinates and assigned stable identifiers of the form PAp00000001.
Builds are made per organism and for important sample groups, such as human plasma, urine, HLA peptidome and post-translational modification enrichments (phospho, acetyl, methyl, SUMO and ubiquitin). The build index (main.cgi?output_format=json) listed 110 builds on 2026-10-04. Each build has a download page with peptide FASTA files, tab-separated tables, a MySQL dump and coordinate mappings. Download URLs include the build date (for example builds/human/202601/), so the products here point to the Human 2026-01 build (atlas build 607) and must be updated when a new build appears.
The site states “All Rights Reserved” in its footer and no data license was found on 2026-10-04.
Created: October 04, 2026 | Last modified: October 04, 2026