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Proteomics2014; 14(6); 763-773; doi: 10.1002/pmic.201300398

The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research.

Abstract: Progress in MS-based methods for veterinary research and diagnostics is lagging behind compared to the human research, and proteome data of domestic animals is still not well represented in open source data repositories. This is particularly true for the equine species. Here we present a first Equine PeptideAtlas encompassing high-resolution tandem MS analyses of 51 samples representing a selection of equine tissues and body fluids from healthy and diseased animals. The raw data were processed through the Trans-Proteomic Pipeline to yield high quality identification of proteins and peptides. The current release comprises 24 131 distinct peptides representing 2636 canonical proteins observed at false discovery rates of 0.2% at the peptide level and 1.4% at the protein level. Data from the Equine PeptideAtlas are available for experimental planning, validation of new datasets, and as a proteomic data mining resource. The advantages of the Equine PeptideAtlas are demonstrated by examples of mining the contents for information on potential and well-known equine acute phase proteins, which have extensive general interest in the veterinary clinic. The extracted information will support further analyses, and emphasizes the value of the Equine PeptideAtlas as a resource for the design of targeted quantitative proteomic studies.
© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Publication Date: 2014-02-16 PubMed ID: 24436130PubMed Central: PMC4340707DOI: 10.1002/pmic.201300398Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • N.I.H.
  • Extramural
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  • Non-U.S. Gov't
  • Research Support
  • U.S. Gov't
  • Non-P.H.S.

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research presents the first Equine PeptideAtlas, a database for peptide and protein mapping in horses. It serves as an open-source repository for proteomics-based veterinary research and can be used to plan experiments, validate new datasets, and mine proteomic data.

Research Background and Objective

  • The research is based on Mass Spectrometry (MS)-derived methods for veterinary research, especially for the equine species.
  • The objective was to create an open-source repository for proteome data of domestic animals, specifically horses, as such data was not well-represented in existing databases.

Methodology

  • The researchers conducted high-resolution tandem MS analyses of 51 samples taken from equine tissues and body fluids.
  • These samples were collected from both healthy and diseased horses.
  • The raw data from these samples were processed through a Trans-Proteomic Pipeline to accurately identify proteins and peptides.

Findings

  • The Equine PeptideAtlas comprises 24,131 distinct peptides that represent 2,636 canonical proteins.
  • It operates with a false discovery rate of 0.2% at the peptide level, and 1.4% at the protein level, indicating a high level of reliability.
  • The Atlas serves as a resource for designing targeted quantitative proteomic studies, experimental planning, data mining, and for validation of new datasets.

Significance and Demonstration of the Atlas’ Advantages

  • Examples of the Atlas’ usefulness include mining data for information on potential and known equine acute phase proteins, which are of interest in veterinary clinics.
  • The curated data from the Atlas supports detailed analyses, reinforcing the value of the Equine PeptideAtlas as a resource for proteomics-based veterinary research.

Cite This Article

APA
Bundgaard L, Jacobsen S, Sørensen MA, Sun Z, Deutsch EW, Moritz RL, Bendixen E. (2014). The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research. Proteomics, 14(6), 763-773. https://doi.org/10.1002/pmic.201300398

Publication

Proteomics
ISSN: 1615-9861
NlmUniqueID: 101092707
Country: Germany
Language: English
Volume: 14
Issue: 6
Pages: 763-773

Researcher Affiliations

Bundgaard, Louise
  • Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark.
Jacobsen, Stine
    Sørensen, Mette A
      Sun, Zhi
        Deutsch, Eric W
          Moritz, Robert L
            Bendixen, Emøke

              MeSH Terms

              • Amino Acid Sequence
              • Animals
              • Data Mining
              • Databases, Protein
              • Horse Diseases / metabolism
              • Horses / metabolism
              • Humans
              • Molecular Sequence Data
              • Peptides / analysis
              • Peptides / metabolism
              • Proteome / analysis
              • Proteome / metabolism
              • Proteomics / methods
              • Tandem Mass Spectrometry / methods

              Grant Funding

              • P50 GM076547 / NIGMS NIH HHS
              • R01 GM087221 / NIGMS NIH HHS
              • RC2 HG005805 / NHGRI NIH HHS
              • 2P50 GM076547 / NIGMS NIH HHS

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