Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues.

Author(s): Hwang SI, Thumar J, Lundgren DH, Rezaul K, Mayya V, Wu L, Eng J, Wright ME, Han DK

Publication: Oncogene, 2007, Vol. 26, Page 65-76

PubMed ID: 16799640 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the relative efficiencies of extraction buffers used for protein recovery in a PFPE coronary artery specimen and prostate tissue array specimens.

   Summary of Findings:

   Using PFPE coronary artery, only 13.5% as much protein was extracted using a buffer containing 30% acetonitrile and 100 mM ammonium bicarbonate (buffer A) as was extracted using a solution containing 2% sodium dodecyl sulfate in radioimmunoprecipitation assay buffer (buffer D). Using PFPE prostate tissue arrays, 47.4% of the protein extracted with buffer D was extracted with buffer A, while 77% more protein was extracted with 0.1% RapiGest in 50 mM NH4HCO3 (buffer E) than with buffer D. The authors conclude that if enough specimen is available, buffer D should be used preferentially, but buffer A is compatible with liquid chromatography mass spectrophotometry.

   Biospecimens

   • Tissue - Prostate
   • Tissue - Blood Vessel

   Preservative Types

   • Other Preservative

   Diagnoses:

   • Normal
   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   Protein	1D/2D gels

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Analyte Extraction and Purification	Analyte isolation method	0.1% RapiGest in 50 mM NH4HCO3 30% acetonitrile and 100 mM ammonium bicarbonate, 2% sodium dodecyl sulfate in radioimmunoprecipitation assay (RIPA) buffer
   Biospecimen Acquisition	Biospecimen location	Prostate Coronary artery

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