In addition to the open-source R packages and R-Shiny applications, we explore the performance of the popular tool Perseus for those users that uses the MaxQuant framework. Perseus 21 () is the chosen tool from the MaxQuant ecosystem for downstream analysis of quantitative results. Perseus is a desktop application which offers a wide variety of algorithms for MaxQuant data normalization, imputation, bash correction and differential expression analysis. The input of the tool is the proteinGroups.txt file output of MaxQuant and can't be used for any other software. Users need to manually annotate the condition during data processing and can choose the raw intensities, LFQ intensity or IBAQ values for the analysis. It provides quality control reports but requires users to generate them manually. The tool provides an extensive number of supporting materials and online tutorials; however, it can be daunting to newcomers and requires a significant time investment as it is not immediately evident which steps are required .