VisioProt-MS: interactive 2D maps from intact protein mass spectrometry

Bioinformatics. 2019 Feb 15;35(4):679-681. doi: 10.1093/bioinformatics/bty680.


Summary: VisioProt-MS is designed to summarize and analyze intact protein and top-down proteomics data. It plots the molecular weights of eluting proteins as a function of their retention time, thereby allowing inspection of runs from liquid chromatography coupled to mass spectrometry (LC-MS). It also overlays MS/MS identification results. VisioProt-MS is compatible with outputs from many different top-down dedicated software. To our knowledge, this is the only open source standalone application that allows the dynamic comparison of several MS files, a prerequisite for comparative analysis of different biological conditions. With its dynamic rendering, this user-friendly web application facilitates inspection, comparison and export of publication quality 2 D maps from deconvoluted LC-MS run(s) and top-down proteomics data.

Availability and implementation: The Shiny-based web application VisioProt-MS is suitable for non-R users. It can be found at and the corresponding scripts are downloadable at It is governed by the CeCILL license (

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Liquid
  • Mass Spectrometry
  • Proteins / chemistry*
  • Proteomics*
  • Software


  • Proteins