Analysis of the human urine endogenous peptides by nanoparticle extraction and mass spectrometry identification

[Display omitted] •Human urine peptides were selectively enriched by mesoporous nanoparticles.•The extracted peptides were pre-fractionated by size exclusion chromatography.•The pH of urine should be kept at its native state to avoid protein proteolysis. Peptides in urine are excreted by kidney from the blood and tissues, which are composed of a large amount of hormones, cytokines, regulatory factors and the metabolized fragments of proteins. The peptide distribution in urine will reflect the physiological and pathophysiological processes in body. In past, limited information was reported about the composition of the peptides in urine. One possible reason is that the peptides in urine are fairly low abundant and there are high concentrations of salts and organic metabolites in the urine. In this report, we extracted the peptides from human urine by highly ordered mesoporous silica particles with the pore size of 2nm, which will exclude the high molecular weight proteins over 12kDa. The extracted peptides were then separated into fractions according to their molecular weight by size exclusion chromatography. Each of the fractions was further analyzed by MALDI-TOF MS and μRPLC–MS/MS. Totally, 193 peptides were identified by two-dimensional SEC/μRPLC–MS/MS analysis. By analyzing the progenitor protein of the peptides; we found that two-thirds of the proteins differed from the reported urine proteome database, and the high abundant proteins in urine proteome were less detected in the urine peptidome. The developed extraction and separation methods were efficient for the profiling of the endogenous peptides in human urine. The peptidome in human urine was complementary to the human urinary proteome and may provide an emerging field for biomarker discovery.