Background <p>Polysome profiling is a widespread technique to study mRNA translation. After separation of cellular particles by ultracentrifugation on a sucrose-density gradient, a UV absorbance profile is recorded during elution, which mostly reflects RNA content and shows distinct peaks for ribosomal subunits, monosomes and polysomes with increasing number of ribosomes. This profile can be used to assess global translational activity, or to reveal changes in ribosome biogenesis and translation elongation. In addition, it is also possible to measure the association of fluorescently tagged proteins with ribosomal subunits or polysomes. Alignment and quantification of polysome profiles usually relies on spreadsheet programs, custom R/Python scripts or commercial software.</p> Results <p>With QuAPPro, we present the first interactive web app that allows quantification and alignment of polysome profiles, independently of the device or software that was used to generate the profiles. QuAPPro was written in R, with a graphical user interface implemented in R shiny. It supports interactive visualization and analysis of polysome profiles, including profile smoothing, baseline selection, alignment along a defined point on the x-axis, quantification of profile subsections and deconvolution for resolving individual peaks. Fluorescence profiles can be aligned and quantified in parallel. Finally, quantification results can be summarized and visualized as bar plots. Every interactive plot can be exported directly in a publication-ready format.</p> Conclusions <p>This user-friendly tool does not only speed up the analysis of polysome profiles but also facilitates reproducibility and documentation of the process, without the need for programming abilities or commercial software.</p>