The LFQ-based dataset (PXD000279) was used to evaluate the different processing steps and performance of every described package. In summary, this dataset consists of two E. coli digested samples (with 4 replicates for each sample); each half of the samples enriched with one of two "Universal Protein Standards" (UPS1 and UPS2). Both samples contain the same 48 recombinant human proteins, which were either mixed in equal amounts (UPS1) or spanned multiple orders of magnitude at a determined ratio (UPS2). Based on the experimental design, 40 of the 48 UPS proteins and none of the E. coli proteins should be detected as differentially expressed. This dataset has been extensively used to evaluate LFQ-based differential expression tools 15, 25, 28 and algorithms . We used dataset PXD000279 mainly to study the performance of the different tools based on protein-intensity information as input.