title: Exploring the potential of public proteomics data.
abstract: In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re-)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
authors.affiliation: Medical Biotechnology Center, VIB, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.|Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Verheggen
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Attila
authors.initials: A
authors.lastname: Csordas
authors.affiliation: Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway.
authors.forename: Helge
authors.initials: H
authors.lastname: Raeder
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.|Department of Clinical Medicine, KG Jebsen Centre for Multiple Sclerosis Research, University of Bergen, Bergen, Norway.
authors.forename: Frode S
authors.initials: FS
authors.lastname: Berven
authors.affiliation: Medical Biotechnology Center, VIB, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.|Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Juan A
authors.initials: JA
authors.lastname: Vizcaíno
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.|Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway.
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
mesh_terms: D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D033181:Information Dissemination; D051188:Knowledge Bases; D058977:Molecular Sequence Annotation; D011499:Protein Processing, Post-Translational; D040901:Proteomics
keywords: Bioinformatics; Computational proteomics; Data analysis; Data standards; Databases