title: A Golden Age for Working with Public Proteomics Data.
abstract: Data sharing in mass spectrometry (MS)-based proteomics is becoming a common scientific practice, as is now common in the case of other, more mature 'omics' disciplines like genomics and transcriptomics. We want to highlight that this situation, unprecedented in the field, opens a plethora of opportunities for data scientists. First, we explain in some detail some of the work already achieved, such as systematic reanalysis efforts. We also explain existing applications of public proteomics data, such as proteogenomics and the creation of spectral libraries and spectral archives. Finally, we discuss the main existing challenges and mention the first attempts to combine public proteomics data with other types of omics data sets.
authors.affiliation: Medical Biotechnology Center, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium. Electronic address: lennart.martens@vib-ugent.be.
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 CB10 1SD, UK. Electronic address: juan@ebi.ac.uk.
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
mesh_terms: D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry; D040901:Proteomics