Proteus () is used for downstream analysis of MaxQuant output data, and differential expression analysis based on the popular algorithms and package limma . Proteus supports two normalization methods: equalize median and quantile, and it uses a mean-variance relationship to estimate variance (limma) where data are missing. The Proteus Shiny application allows users to perform the analysis with one click if the data is provided in the MaxQuant format. Shiny-based volcano plots and fold-change intensity plots enable users to interact with differentially expressed proteins of interest and view the results in detail for statistically significant results. One of the other advantages of the package is the number of data processing parameters which enables non-expert users to perform a robust analysis of their data without the need to try multiple combinations of parameters. However, no quality control (QC) metrics or plots are provided by the package making it difficult to assess the quality and reproducibility of the experiment.