TopDownApp: An open and modular platform for analysis and visualisation
of top-down proteomics data
Abstract
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.