The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array

J Proteomics. 2010 Jan 3;73(3):649-66. doi: 10.1016/j.jprot.2009.09.004. Epub 2009 Sep 13.


Blood-based protein biomarkers hold great promise to advance medicine with applications that detect and diagnose diseases and aid in their treatment. We are developing such applications with our proteomics technology that combines high-content with low limits of detection. Biomarker discovery relies heavily on archived blood sample collections. Blood is dynamic and changes with different sampling procedures potentially confounding biomarker studies. In order to better understand the effects of sampling procedures on the circulating proteome, we studied three sample collection variables commonly encountered in archived sample sets. These variables included (1) three different sample tube types, PPT plasma, SST serum, and Red Top serum, (2) the time from venipuncture to centrifugation, and (3) the time from centrifugation to freezing. We profiled 498 proteins for each of 240 samples and compared the results by ANOVA. The results found no significant variation in the measurements for most proteins (approximately 99%) when the two sample processing times tested were 2h or less, regardless of sample tube type. Even at the longest timepoints, 20 h, approximately 82% of the proteins, on average for the three collection tube types, showed no significant change. These results are encouraging for proteomic biomarker discovery.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Aptamers, Peptide / chemistry
  • Blood Coagulation / physiology
  • Blood Preservation / adverse effects
  • Blood Preservation / methods
  • Blood Proteins / analysis
  • Blood Proteins / metabolism*
  • Blood Specimen Collection / adverse effects
  • Blood Specimen Collection / methods*
  • Blood Specimen Collection / standards
  • Cluster Analysis
  • Freezing / adverse effects
  • Humans
  • Models, Biological
  • Observer Variation
  • Protein Array Analysis / instrumentation
  • Protein Array Analysis / methods
  • Protein Stability*
  • Proteome / analysis*
  • Proteome / metabolism*
  • Proteomics / instrumentation
  • Proteomics / methods
  • SELEX Aptamer Technique / instrumentation
  • SELEX Aptamer Technique / methods*
  • Time Factors


  • Aptamers, Peptide
  • Blood Proteins
  • Proteome