title: PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks.
abstract: Protein phosphorylation is an essential post-translational modification (PTM) regulating many biological processes at the cellular and multicellular level. Continuous improvements in phosphoproteomics technology allow the analysis of this PTM in an expanding biological content, yet up until now proteome data visualization tools are still very gene centric, hampering the ability to comprehensively map and study PTM dynamics. Here we present PhosphoPath, a Cytoscape app designed for the visualization and analysis of quantitative proteome and phosphoproteome data sets. PhosphoPath brings knowledge into the biological network by importing publically available data and enables PTM site-specific visualization of information from quantitative time series. To showcase PhosphoPath performance we use a quantitative proteomics data set comparing patient-derived melanoma cell lines grown in either conventional cell culture or xenografts.
authors: Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.|Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors: Linsey M
authors: LM
authors: Raaijmakers
authors: Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.|Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors: Piero
authors: P
authors: Giansanti
authors: Division of Molecular Oncology, The Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands.
authors: Patricia A
authors: PA
authors: Possik
authors: Division of Molecular Oncology, The Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands.
authors: Judith
authors: J
authors: Mueller
authors: Division of Molecular Oncology, The Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands.
authors: Daniel S
authors: DS
authors: Peeper
authors: Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.|Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors: Albert J R
authors: AJ
authors: Heck
authors: Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.|Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors: A F Maarten
authors: AF
authors: Altelaar
mesh_terms: D045744:Cell Line, Tumor; D003196:Computer Graphics; D053263:Gene Regulatory Networks; D006801:Humans; D008545:Melanoma / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D063731:Mobile Applications; D010750:Phosphoproteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D040901:Proteomics; D012878:Skin Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D053719:Tandem Mass Spectrometry
chemical_list: D010750:Phosphoproteins; D020543:Proteome
keywords: Cytoscape; biological network analysis; computational proteomics; phosphoproteomics; phosphosite-centric dynamics; posttranslational modifications; signaling