Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome

J Proteome Res. 2011 Feb 4;10(2):637-45. doi: 10.1021/pr100835s. Epub 2011 Jan 5.

Abstract

Urine is a readily and noninvasively obtainable body fluid. Mass spectrometry (MS)-based proteomics has shown that urine contains thousands of proteins. Urine is a potential source of biomarkers for diseases of proximal and distal tissues but it is thought to be more variable than the more commonly used plasma. By LC-MS/MS analysis on an LTQ-Orbitrap without prefractionation we characterized the urinary proteome of seven normal human donors over three consecutive days. Label-free quantification of triplicate single runs covered the urinary proteome to a depth of more than 600 proteins. The median coefficient of variation (cv) of technical replicates was 0.18. Interday variability was markedly higher with a cv of 0.48 and the overall variation of the urinary proteome between individuals was 0.66. Thus technical variability in our data was 7.5%, whereas intrapersonal variability contributed 45.5% and interpersonal variability contributed 47.1% to total variability. Determination of the normal fluctuation of individual urinary proteins should be useful in establishing significance thresholds in biomarker studies. Our data also allowed definition of a common and abundant set of 500 proteins that were readily detectable in all studied individuals. This core urinary proteome has a high proportion of secreted, membrane, and relatively high-molecular weight proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Liquid
  • Computational Biology
  • Humans
  • Peptide Fragments / analysis
  • Peptide Fragments / metabolism
  • Proteins / analysis
  • Proteins / metabolism
  • Proteinuria / urine*
  • Proteome / analysis*
  • Proteome / metabolism
  • Reproducibility of Results
  • Statistics, Nonparametric
  • Tandem Mass Spectrometry
  • Urine / chemistry*

Substances

  • Peptide Fragments
  • Proteins
  • Proteome