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Protter: interactive protein feature visualization and integration with experimental proteomic data.

Ulrich Omasits1, Christian H Ahrens, Sebastian Müller

  • 1Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich and Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland.

Bioinformatics (Oxford, England)
|October 29, 2013
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Summary
This summary is machine-generated.

Protter is a new web tool that integrates and visualizes proteomic data with protein annotations. This tool aids researchers in analyzing protein data and generating hypotheses, especially for membrane proteins.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Integrating and visualizing experimental proteomic evidence with protein annotations is a significant challenge.
  • Existing tools lack comprehensive visualization of protein topology alongside experimental data.

Purpose of the Study:

  • To introduce Protter, a web-based tool for interactive protein data analysis.
  • To address the unmet need for visualizing proteomic evidence within the context of protein features and topology.

Main Methods:

  • Developed Protter as a web application supporting interactive analysis.
  • Integrated numerous proteomic file formats and diverse protein annotation sources.
  • Enabled extension via modular plug-ins and provided export functions for publication-quality illustrations.

Main Results:

  • Protter facilitates interactive protein data analysis and hypothesis generation.
  • The tool visualizes annotated sequence features and experimental proteomic data in protein topology context.
  • Demonstrated utility for surfaceome datasets, membrane proteins, and targeted proteomics peptide selection.

Conclusions:

  • Protter effectively integrates and visualizes proteomic evidence with rich protein annotations.
  • The tool enhances the analysis of membrane proteins and aids in peptide selection for targeted proteomics.
  • Protter supports hypothesis generation and publication-quality data visualization for the proteomics community.