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TopDownApp: An open and modular platform for analysis and visualisation of top-down proteomics data
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  • Mathias Walzer,
  • Kyowon Jeong,
  • David L. Tabb,
  • Juan Antonio Vizcaino
Mathias Walzer
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Kyowon Jeong
University of Tubingen Faculty of Science
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David L. Tabb
Institut Pasteur
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Juan Antonio Vizcaino

Corresponding Author:[email protected]

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Although Top-down (TD) proteomics techniques, aimed at the analysis of intact proteins and proteoforms, are becoming increasingly popular, efforts are needed at different levels to generalise its adoption. In this context, there are numerous improvements that are possible in the area of open science including the FAIR (Findability, Accessibility, Interoperability and Reusability) data principles. These include e.g. increased data sharing practices and availability of tailored open data standards. Additionally, the field would benefit from the development of open analysis workflows that can enable e.g. data reuse of public datasets, something that is increasingly common in other proteomics fields. We present an open and modular platform for the analysis and visualisation of TD proteomics data called TopDownApp. It can be used as a flexible analysis platform, through the use of a common workflow engine, common data formats for input/output, and software containerisation. It can also serve as a tool for visual inspection through its simple setup. As a key point, it can also be used as a development platform for new tools through the use of Python, a modular design, software containerisation and common data formats. TopDownApp is open source and freely available at: https://github.com/mwalzer/TopDownApp.
02 Jun 2023Submitted to PROTEOMICS
06 Jun 2023Assigned to Editor
06 Jun 2023Submission Checks Completed
06 Jun 2023Review(s) Completed, Editorial Evaluation Pending
06 Jun 2023Reviewer(s) Assigned
11 Jul 2023Editorial Decision: Revise Minor
13 Sep 2023Review(s) Completed, Editorial Evaluation Pending
13 Sep 20231st Revision Received
13 Sep 2023Editorial Decision: Accept