The results highlighted that no major differences are observed when protein level intensity from MaxQuant is used. Most of the tools can correctly quantify the true positive with low false positive rates, however, MSstats was the tool that performed best among the benchmarked packages. We used Proteus and MSstats to evaluate the performance of protein quantification based on peptide-level intensities data from the quantms workflow. Overall, for both datasets analyzed PXD007145 and PXD020248; MSstats provides lower CVs across replicates and more accuracy to quantify the correct differential expression ratios in dataset PXD007145. However, we observed that when the datasets presented higher CV values independently of the tools used for the analysis the results are not consistent and difficult to compare across tools. This fact should trigger a more rigorous study in the figure and possible guidelines about the number of technical/biological replicates or expected CVs in one proteomics LFQ experiment to be the quantitative results reproducible and accurate, even if they pass the author's specific statistical tests.