title: Visualizing meta-features in proteomic maps.
abstract: BACKGROUND
  The steps of a high-throughput proteomics experiment include the separation, differential expression and mass spectrometry-based identification of proteins. However, the last and more challenging step is inferring the biological role of the identified proteins through their association with interaction networks, biological pathways, analysis of the effect of post-translational modifications, and other protein-related information.
  
  
  RESULTS
  In this paper, we present an integrative visualization methodology that allows combining experimentally produced proteomic features with protein meta-features, typically coming from meta-analysis tools and databases, in synthetic Proteomic Feature Maps. Using three proteomics analysis scenarios, we show that the proposed visualization approach is effective in filtering, navigating and interacting with the proteomics data in order to address visually challenging biological questions. The novelty of our approach lies in the ease of integration of any user-defined proteomic features in easy-to-comprehend visual representations that resemble the familiar 2D-gel images, and can be adapted to the user's needs. The main capabilities of the developed VIP software, which implements the presented visualization methodology, are also highlighted and discussed.
  
  
  CONCLUSIONS
  By using this visualization and the associated VIP software, researchers can explore a complex heterogeneous proteomics dataset from different perspectives in order to address visually important biological queries and formulate new hypotheses for further investigation. VIP is freely available at http://pelopas.uop.gr/~egian/VIP/index.html.
authors.affiliation: HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY 10021, USA. eug2002@med.cornell.edu
authors.forename: Eugenia G
authors.initials: EG
authors.lastname: Giannopoulou
authors.forename: George
authors.initials: G
authors.lastname: Lepouras
authors.forename: Elias S
authors.initials: ES
authors.lastname: Manolakos
mesh_terms: D013058:Mass Spectrometry / Q000379:methods; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins