To explore the performance of tools based on peptide intensity tables we used datasets PXD007145 29 and PXD020248 . ProteomeXchange dataset PXD007145 was used to evaluate the performance based on peptide analysis. It is a multiple species mixture label-free dataset, in which yeast proteome was diluted in fixed ratios of 1:4:10 and added to a background of 1:1:1 human proteome to simulate real experimental data. Six technical replicates were used for each sample to calculate the coefficient of variations. PXD020248 is a cell line hepatocytes sample (HepG2) treated with benzo[a]pyrene (BaP) using a concentration of 2 μM. The original manuscript benchmarked TMT and LFQ analytical methods using the same sample. In the present study, we used the LFQ part of the dataset to benchmark the peptide intensity-based algorithms MSstats and Proteus.