Subject area	Biology
More specific subject area	Characterization of urine proteome in normal conditions. It was developed a new strategy of analysis which allowed the extension of the number of identified proteins to 3429 (1724 were of new description here). The list of identified proteins is reported in Supplementary Table 1.
Type of data	Excel tables
How data was acquired	Ultracentrifuge: Beckman OptimaTM l-90K (Ti 90 rotor).
	Mass spectroscopy: for analysis of all urinary sub-fractions was used a linear Trap Quadropole (LTQ) Orbitrap Velos Pro Mass Spectrometry.
Data format	Raw MS files as processed with the Thermo Scientific Proteome Discoverer software: peak were searched by the MASCOT and SEQUEST against Uniprot human database, filtered for a maximum 1% FDR using Percolator; the Peptide Mass Deviation was set to 10 ppm and a minimum of six 6 amino acids per identified peptide were required [2,3]. The Database search parameters were mass tolerance precursor 20 ppm [4], mass tolerance fragment CID 0.8 Da with dynamic modification of deamidation (N, Q), oxidation (M) and static modification of alkylation with IAM (C).
	Label free experiments and statistical analysis were performed with Perseus software.
Experimental factors	Sample Collection and Urine Preparation: Second morning urine (approximately 160 mL) from healthy volunteers were collected, centrifuged at 4 °C for 10 min at 1000g. Urine were frozen and maintained at −80 until further processing [5–14]. Second step was centrifugation at 17,000g for 30 min at 16 °C. The sample, after Bradford protein assay [15], was stored at −80 °C until use.
Experimental features	Procedure used for analysis of the urinary proteome: Vesicle Isolation, butanol precipitation, Combinatorial Solid-Phase Ligand Library chromatography, Mass spectrometry and Bioinformatic analysis.
Consent	Informed consent was obtained from all the participants in the study.
Data source location	Genova, Italy.
Data accessibility	The data are available at ChorusProject.org under project name “From hundreds to thousands: widening the normal human Urinome”. Row data relative to MS spectra are available at ChorusProject.org under project name “From hundreds to thousands: widening the normal human Urinome”. Data are also directly available with this article