About

The Human PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry (MS) proteomics datasets.

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

PSM stands for Peptide Spectrum Match. It refers to the matching of a spectrum generated from a mass spectrometry experiment to a peptide sequence from a protein database. More ▲

In a typical proteomics experiment, proteins are first digested into peptides using enzymes such as trypsin. These peptides are then separated and ionized before being introduced into a mass spectrometer for analysis. The mass spectrometer generates a spectrum of the ionized peptides, which is then searched against a database of protein sequences to identify the proteins present in the sample.

Each identified peptide sequence generates a PSM, which represents the match between the experimental spectrum and the theoretical spectrum generated from the peptide sequence. PSMs are commonly used to filter and validate peptide identifications, as they provide a measure of the quality of the match between the experimental data and the database search results.

PSMs PER BUILD TYPE

Full 2025-01 Build Summary

806	datasets
3,104	experiments
176,749	MS runs
5,637,324,959	spectra searched
1,114,541,317	PSMs
4,187,316	distinct peptides
17,359	canonical core proteins

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PeptideAtlas and the Chromosome-Centric Human Proteome Project

Chromosome Explorer

Human non-HLA
PeptideAtlas

Human HLA
PeptideAtlas

BROWSE

Human Plasma
PeptideAtlas

Human Plasma
Extracellular Vesicle

Human Urine
PeptideAtlas

Human Phospho
PeptideAtlas

Chromosome Summary

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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

Latest publication: Omenn GS, Lane L, Overall CM, Pineau C, Packer NH, Cristea IM, Lindskog C, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Liu S, Bandeira N, Chen YJ, Guo T, Aebersold R, Moritz RL, Deutsch EW. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project; J Proteome Res. 2022 Nov 1. doi: 10.1021/acs.jproteome.2c00498. PMID: 36318223,
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
Schwenk et al., The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays, Journal of Proteome Research (2017)
Deutsch et al., State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet., Journal of Proteome Research (2015)
Farrah, et al., State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project, Journal of Proteome Research (2014)
Farrah, et al., The State of the Human Proteome in 2012 as Viewed through PeptideAtlas, Journal of Proteome Research, 2013, 12 (1), pp162-171 - [PDF]
Initial publication: Desiere et al., Integration of Peptide Sequences Obtained by High-Throughput Mass Spectrometry with the Human Genome, Genome Biology 2004, 6:R9 - [PDF]

Download

Below are individual Human 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 2025-01 PSM FDR = 0.0001Latest Build

Biosequence Set in FASTA format [566MB]
Database tables exported as TSV dump file [4GB]
Database tables exported as mysql dump file [4GB]
Peptide CDS and chromosomal coordinates [10GB]
Peptide CDS coordinates [6GB]
Peptide sequences in FASTA format [125MB]

Human 2024-01 PSM FDR = 0.0001

Biosequence Set in FASTA format [740MB]
Database tables exported as TSV dump file [4GB]
Database tables exported as mysql dump file [3GB]
Peptide CDS and chromosomal coordinates [10GB]
Peptide CDS coordinates [6GB]
Peptide sequences in FASTA format [117MB]

View Older Downloads ▲

Human 2023-01 PSM FDR = 0.0001

Biosequence Set in FASTA format [633MB]
Database tables exported as TSV dump file [3GB]
Database tables exported as mysql dump file [2GB]
Peptide CDS and chromosomal coordinates [7GB]
Peptide CDS coordinates [4GB]
Peptide sequences in FASTA format [103MB]

Human 2022-01 PSM FDR = 0.0001

Biosequence Set in FASTA format [598MB]
Database tables exported as TSV dump file [3GB]
Database tables exported as mysql dump file [2GB]
Peptide CDS and chromosomal coordinates [5GB]
Peptide CDS coordinates [3GB]
Peptide sequences in FASTA format [86MB]

Human 2021-01 PSM FDR = 0.00015

Biosequence Set in FASTA format [511MB]
Database tables exported as TSV dump file [5GB]
Database tables exported as mysql dump file [4GB]
Peptide CDS and chromosomal coordinates [4GB]
Peptide CDS coordinates [2GB]
Peptide sequences in FASTA format [73MB]

Human 2020-01 PSM FDR = 0.0002

Biosequence Set in FASTA format [449MB]
Database tables exported as TSV dump file [2GB]
Database tables exported as mysql dump file [2GB]
Peptide CDS and chromosomal coordinates [4GB]
Peptide CDS coordinates [2GB]
Peptide sequences in FASTA format [71MB]

Human 2019-01 PSM FDR = 0.0002

Biosequence Set in FASTA format [2GB]
Database tables exported as TSV dump file [63MB]
Database tables exported as mysql dump file [62MB]
Peptide CDS and chromosomal coordinates [2GB]
Peptide CDS coordinates [1GB]
Peptide sequences in FASTA format [51MB]

Human 2016-12 PSM FDR = 0.0002

Biosequence Set in FASTA format [3GB]
Database tables exported as an XML file [2GB]
Peptide CDS and chromosomal coordinates [212MB]
Peptide CDS coordinates [941MB]
Peptide sequences in FASTA format [34MB]

Human 2016-01 PSM FDR = 0.0002

Biosequence Set in FASTA format [7GB]
Database tables exported as an XML file [2GB]
Database tables exported as mysql dump file [1GB]
Peptide CDS and chromosomal coordinates [1GB]
Peptide CDS coordinates [991MB]
Peptide sequences in FASTA format [33MB]

Help

Complete description of each of the available download formats

Non-canonical ORFs

PeptideAtlas has been searching for translation evidence for non-canonical ORFs (ncORFs) using sequences of 7264 ncORFs detected by Ribo-seq datasets as published by Mudge et al. (2021).

Download FASTA file of 7264 Ribo-seq ncORFs

Other Resources

Acknowledgements

We gratefully acknowledge the support for the Human PeptideAtlas from NIGMS grants R01GM087221 and R24GM127667.