title: The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine.
abstract: Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this article demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research.
authors.affiliation: Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
authors.forename: Marianne O
authors.initials: MO
authors.lastname: Hesselager
authors.affiliation: Quantitative Biology Center (QBiC), Eberhard Karls Universität, Tübingen, Germany.
authors.forename: Marius C
authors.initials: MC
authors.lastname: Codrea
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.affiliation: Department of Health Science and Technology, Aalborg University, Aalborg, Denmark.
authors.forename: Tue B
authors.initials: TB
authors.lastname: Bennike
authors.affiliation: Department of Health Science and Technology, Aalborg University, Aalborg, Denmark.
authors.forename: Allan
authors.initials: A
authors.lastname: Stensballe
authors.affiliation: Department of Large Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Louise
authors.initials: L
authors.lastname: Bundgaard
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.affiliation: Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
authors.forename: Emøke
authors.initials: E
authors.lastname: Bendixen
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D057225:Data Mining; D030562:Databases, Protein; D007249:Inflammation / Q000175:diagnosis / Q000276:immunology / Q000378:metabolism / Q000662:veterinary; D013058:Mass Spectrometry; D053858:Metabolic Networks and Pathways; D020033:Protein Isoforms / Q000032:analysis; D020543:Proteome / Q000032:analysis* / Q000276:immunology / Q000378:metabolism; D040901:Proteomics; D000685:Serum Amyloid A Protein / Q000032:analysis; D034421:Sus scrofa / Q000276:immunology / Q000378:metabolism*; D013552:Swine; D013553:Swine Diseases / Q000175:diagnosis / Q000276:immunology / Q000378:metabolism
chemical_list: D020033:Protein Isoforms; D020543:Proteome; D000685:Serum Amyloid A Protein
keywords: Animal model; Biomarker; Pig PeptideAtlas; Proteomics; Repositories