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PeptideAtlas specifications


Unique identifier OMICS_02454
Name PeptideAtlas
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • ProteoMapper


  • person_outline Eric W. Deutsch

Publications for PeptideAtlas


The PeptideAtlas project

2006 Nucleic Acids Res
PMCID: 1347403
PMID: 16381952
DOI: 10.1093/nar/gkj040

PeptideAtlas citations


Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

Microb Genom
PMCID: 5885015
PMID: 29557774
DOI: 10.1099/mgen.0.000163

[…] 1. RNA-seq datasets have been deposited in ENA; accession number PRJEB23469.2. SWATH MS data and OpenSWATH outputs have been deposited in PeptideAtlas under identifier PASS00685 ( Mycobacterium tuberculosis complex (MTBC) includes the most important global pathogens for humans and animals, […]


The Gene Centric Content Management System and Its Application for Cognitive Proteomics

PMCID: 5874771
PMID: 29473895
DOI: 10.3390/proteomes6010012

[…] C-HPP, the work of the proteome inventory was split among different teams and countries [].At the beginning of the C-HPP there were established resources on proteomic MS-data (PRIDE [], GPMdb [] and PeptideAtlas []); affinity data (Human Protein Atlas []); human proteome data in neXtProt []; and flexible platforms to work with heterogeneous molecular data, such as TAVERNA []. Despite such a repre […]


Large scale intact glycopeptide identification by Mascot database search

Sci Rep
PMCID: 5795011
PMID: 29391424
DOI: 10.1038/s41598-018-20331-2

[…] bove presented results, the LC-MS data sets of the 24 serum samples were also searched against differentially sized custom glycoprotein databases created from (i) all known plasma/serum proteins from PeptideAtlas build 2010 (2421 glycoproteins), (ii) all deamidated proteins identified following PNGaseF treatment of glycopeptides from the same 24 serum samples (280 glycoproteins) and (iii) Swiss-Pr […]


Lysine Succinylation Contributes to Aflatoxin Production and Pathogenicity in Aspergillus flavus*

PMCID: 5836371
PMID: 29298838
DOI: 10.1074/mcp.RA117.000393

[…] reliability of the MS result, all succinylation sites identified at the C-terminal were removed before the bioinformatics analysis. All raw data have been uploaded to the publicly accessible database PeptideAtlas (data set ID PASS00795) ( (, ). […]


Knockout of the epilepsy gene Depdc5 in mice causes severe embryonic dysmorphology with hyperactivity of mTORC1 signalling

Sci Rep
PMCID: 5626732
PMID: 28974734
DOI: 10.1038/s41598-017-12574-2

[…] de AVNGFLADLFTK; m/z 648.3533, collision energy of 26, and an isolation width of 4. Data was analysed using the open source software Skyline where it was compared to a DEPD5 spectral library acquired PeptideAtlas ( The following Skyline settings were used; trypsin digestion, no missed trypsin cleavages, variable modifications of carbamidomethyl and oxidation, […]


Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach

J Proteome Res
PMCID: 5737412
PMID: 28960077
DOI: 10.1021/acs.jproteome.7b00388

[…] er sample in which design these experiments can be guided by the combination of the proteomic and transcriptomic experiments performed in this study.Additionally, the information on resources such as PeptideAtlas and SRM Atlas could help prioritizing missing proteins for further validation. From the 165 one-hit wonder proteins identified in our analysis, we have found other additional unique pepti […]


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PeptideAtlas institution(s)
Institute for Systems Biology, Seattle, WA, USA
PeptideAtlas funding source(s)
Supported by the American Recovery and Reinvestment Act (ARRA) through grant number RC2 HG005805 from the National Institutes of Health NHGRI, the NIGMS (2P50 GM076547 and R01 GM087221), the U.S. National Science Foundation MRI (grant no. 0923536), and the Bill and Melinda Gates Foundation, Global Health Grant Number 0PP1039684.

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