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SWATHAtlas specifications


Unique identifier OMICS_19910
Name SWATHAtlas
Restrictions to use None
Community driven No
Data access File download
User data submission Allowed
Maintained Yes


  • person_outline Ruedi Aebersold
  • person_outline Etienne Caron

Publication for SWATHAtlas

SWATHAtlas citations


Cost effective generation of precise label free quantitative proteomes in high throughput by microLC and data independent acquisition

Sci Rep
PMCID: 5847575
PMID: 29531254
DOI: 10.1038/s41598-018-22610-4

[…] H data quantification was performed in Spectronaut (v. 8.0.9600, Biognosys) using default settings. Publicly available SWATH libraries used were obtained from the Biognosys library repository or from SWATHAtlas.For visualization of chromatographic peaks, data of selected peptides was analyzed in Skyline (v. with SWATH isolation windows detailed in Suppl. Table , and chromatograms of pr […]


A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host pathogen interactions

Sci Rep
PMCID: 5591248
PMID: 28887440
DOI: 10.1038/s41598-017-10059-w

[…] 7 proteins with 25,664 peptides with a length of 7 to 49 amino acids. This final ion library represents approximately 72% of the theoretical S. aureus proteome and is publicly available at http://www.swathatlas.org. The remaining 28% of the S. aureus proteome was not detected either because these proteins are not expressed under the conditions tested, are in too low abundance to be detected by DDA […]


A first dataset toward a standardized community driven global mapping of the human immunopeptidome

PMCID: 4773481
PMID: 26958639
DOI: 10.1016/j.dib.2016.02.016

[…] s were included for library generation (-cT).Below are the command lines that were used to build the standardized HLA allele-specific peptide spectral and assay libraries, which were deposited in the SWATHAtlas database (http://www.swathatlas.org/):•spectrast -cNSpecLib_celltype_allele_fdr_iRT -cICID-QTOF -cTReference_celltype_allele_fdr.txt -cP0.7 -c_IRTiRT.txt -c_IRR iprophet.pep.xml•A consensus […]


Exploring the potential of public proteomics data

PMCID: 4738454
PMID: 26449181
DOI: 10.1002/pmic.201500295

[…] st, it is expected that public deposition of this type of data will significantly increase in the coming years. In fact, there are already dedicated resources in place such as SWATH‐Atlas (http://www.swathatlas.org) that can be used for planning SWATH experiments, for depositing experiments, and for exploring the results of deposited datasets. A particular characteristic of SWATH‐MS data is that, […]


A repository of assays to quantify 10,000 human proteins by SWATH MS

Sci Data
PMCID: 4322573
PMID: 25977788
DOI: 10.1038/sdata.2014.31

[…] The spectral libraries (SpectraST format) and assay libraries (CSV, TraML) are available for different SWATH-MS data analysis tools at the SWATHAtlas with the dataset identifiers SAL00016-35 (Data Citation 2). […]


Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness*

PMCID: 4083113
PMID: 24741114
DOI: 10.1074/mcp.M114.038273

[…] idently identify a target peptide in the SWATH-MS map using a dedicated search tool such as OpenSWATH (). To support this type of data analysis for the N-glycoproteome, we generated an N-glycoprotein SWATHatlas derived from synthetic peptides as an easily transferrable resource that will also support future targeted proteomic studies focused on the N-glycoproteome. The assays from the N-glycoprote […]


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SWATHAtlas institution(s)
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Department of Immunology, Interfaculty Institute for Cell Biology, University of Tubingen, Tubingen, Germany; DKFZ partner site Tubingen, German Cancer Consortium, Tubingen, Germany; Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, UK; Proteomics Unit, Spanish National Biotechnology Centre, Madrid, Spain; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA; Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; Pacific Northwest National Laboratory, Richland, WA, USA; Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Hong Kong, China; Institute for Systems Biology, Seattle, WA, USA; Faculty of Science, University of Zurich, Zurich, Switzerland
SWATHAtlas funding source(s)
Supported by National Health and Medical Research Council (NHMRC) (1022509 and 1085017); National Institutes of Health (NIH) (HHSN272201200010C and HHSN272200900044C); European Research Council (ERC) (ERC-2008-AdG_20080422); Schweizerische Nationalfonds zur Forderung der Wissenschaftlichen Forschung (3100A0-688 107679); European Commission (EC) (SysteMtb, 241587); German Cancer Consortium (DKTK); Bundesministerium fur Bildung und Forschung (e:Bio Express2Present, 0316179C); Forschungszentrum Immuntherapie (FZI) of the Johannes Gutenberg University Mainz; Ministerio de Economıa y Competitividad [Carlos III Health Institute (ISCIII) (ProteoRed-PRB2, PT13/0001)]; European Commission (EC) (Marie Curie IntraEuropean Fellowship); Schweizerische Nationalfonds zur Forderung der Wissenschaftlichen Forschung (Postdoc Mobility Fellowship); National Institute of General Medical Sciences (NIGMS) (R01GM087221 and 2P50 GM076547/Center for Systems Biology).

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