Subject area	Bioinformatics for proteomics
More specific subject area	Label-free quantification of proteomic data
Type of data	MS data, table and figures
How data was acquired	Mass spectrometry (LTQ-Velos data)
Data format	Raw+Excel file (data processed with different bioinformatics workflows)
Experimental factors	Data was obtained from the MS analysis of a proteomic standard formed of a fixed background (yeast cell lysate) spiked with 9 different amounts of the UPS1 standard mixture (Sigma).
Experimental features	Samples corresponding to the 9 different concentrations of UPS1 spiked in yeast lysate were reduced and alkylated, digested with trypsin, and analyzed in triplicate by nanoLC-MS/MS on a LTQ-Velos Orbitrap. Different workflows were applied for data processing and label-free quantification of proteins in pairwise comparison of different UPS1 concentrations.
Data source location	Toulouse, France
Grenoble, France
Strasbourg, France
Data accessibility	All raw MS data is deposited in the ProteomeXchange repository with the identifier PXD001819. Protein quantitative metrics obtained from different bioinformatics workflow are provided in Supplementary Table1.