title: Viewing the proteome: how to visualize proteomics data?
abstract: Proteomics has become one of the main approaches for analyzing and understanding biological systems. Yet similar to other high-throughput analysis methods, the presentation of the large amounts of obtained data in easily interpretable ways remains challenging. In this review, we present an overview of the different ways in which proteomics software supports the visualization and interpretation of proteomics data. The unique challenges and current solutions for visualizing the different aspects of proteomics data, from acquired spectra via protein identification and quantification to pathway analysis, are discussed, and examples of the most useful visualization approaches are highlighted. Finally, we offer our ideas about future directions for proteomics data visualization.
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway; KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway.
authors.forename: Eystein
authors.initials: E
authors.lastname: Oveland
authors.forename: Thilo
authors.initials: T
authors.lastname: Muth
authors.forename: Erdmann
authors.initials: E
authors.lastname: Rapp
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.forename: Frode S
authors.initials: FS
authors.lastname: Berven
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
mesh_terms: D003196:Computer Graphics; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D066264:Datasets as Topic; D006801:Humans; D058977:Molecular Sequence Annotation; D009928:Organ Specificity; D060066:Protein Interaction Maps; D020543:Proteome / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D020543:Proteome
keywords: Bioinformatics; Graphs; Proteome databases; Raw data; Visualization