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
-
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
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