In this study, we explore multiple R-packages and tools for downstream data analysis of LFQ experiments based on protein and peptide intensity results. We explored seven different R or Shiny applications including MSstats, Proteus, prolfqua, ProVision, LFQ-Analyst, Eatomics, ProStaR and the popular C# tool Perseus. Most of these packages (LFQ-Analyst, ProVision, Eatomics, prolfqua) have been created as an alternative to Perseus to analyze the output of MaxQuant in the R. MSstats, Proteus and ProStaR can process not only protein intensity results but peptide-based results which make them more generic solutions to be coupled with other tools such as DIA-NN, quantms, Skyline, etc. MSstats is not only the most well-documented package but also the one with more support. However, other packages like prolfqua have more quality control capabilities which are crucial in differential expression data analysis to detect variances and errors in specific samples or analytical steps.