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J Proteome Res. 2015 Oct 2;14(10):4332-41. doi: 10.1021/acs.jproteome.5b00529. Epub 2015 Sep 8.

PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks.

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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.
Division of Molecular Oncology, The Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands.


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.


Cytoscape; biological network analysis; computational proteomics; phosphoproteomics; phosphosite-centric dynamics; posttranslational modifications; signaling

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