Variability of protein and phosphoprotein levels in clinical tissue specimens during the preanalytical phase

J Proteome Res. 2012 Dec 7;11(12):5748-62. doi: 10.1021/pr300560y. Epub 2012 Nov 16.


The quality of human tissue specimens can have a significant impact on analytical data sets for biomarker research. The aim of this study was to characterize fluctuations of protein and phosphoprotein levels in human tissue samples during the preanalytical phase. Eleven intestine and 17 liver specimens were surgically resected, aliquoted, and either snap-frozen or fixed in formalin immediately or exposed to different ischemic conditions before preservation. Protein levels in the resultant samples were investigated by reverse phase protein array, Western blot analysis, and liquid chromatography-tandem mass spectrometry. Our data revealed that the degree of sensitivity of proteins and phosphoproteins to delayed preservation varied between different patients and tissue types. For example, up-regulation of phospho-p42/44 MAPK in intestine samples was seen in some patients but not in others. General trends toward up- or down-regulation of most proteins were not evident due to pronounced interpatient variability but signal intensities of only a few proteins, such as cytokeratin 18, were altered from baseline in postresection samples. In contrast, glyceraldehyde 3-phosphate dehydrogenase was found to be stable during periods of cold ischemia. Our study represents a proper approach for studying potential protein fluctuations in tissue specimens for future biomarker development programs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomarkers, Tumor / analysis*
  • Biomarkers, Tumor / metabolism
  • Biopsy / methods
  • Blotting, Western
  • Chromatography, Liquid
  • Cold Ischemia
  • Colon / metabolism
  • Colon / pathology*
  • Colonic Neoplasms / chemistry
  • Colonic Neoplasms / diagnosis
  • Colonic Neoplasms / pathology
  • Cryopreservation / methods
  • Formaldehyde / chemistry
  • Humans
  • Intestine, Small / metabolism
  • Keratin-18 / analysis
  • Keratin-18 / metabolism
  • Liver / metabolism
  • Liver / pathology*
  • Liver Neoplasms / secondary
  • Mitogen-Activated Protein Kinase 1 / analysis
  • Mitogen-Activated Protein Kinase 1 / metabolism
  • Neoplasm Metastasis / pathology
  • Neoplasm Proteins / analysis*
  • Neoplasm Proteins / metabolism
  • Phosphoproteins / analysis*
  • Phosphoproteins / metabolism
  • Protein Array Analysis
  • Proteome / analysis
  • Proteome / metabolism
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Tandem Mass Spectrometry
  • Time Factors
  • Tissue Fixation / methods*
  • Warm Ischemia / methods


  • Biomarkers, Tumor
  • Keratin-18
  • Neoplasm Proteins
  • Phosphoproteins
  • Proteome
  • Formaldehyde
  • MAPK1 protein, human
  • Mitogen-Activated Protein Kinase 1