Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

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Proteomics out of the archive: Two-dimensional electrophoresis and mass spectrometry using HOPE-fixed, paraffin-embedded tissues.

Author(s): Kähler D, Alexander C, Schultz H, Abdullah M, Branscheid D, Lindner B, Zabel P, Vollmer E, Goldmann T

Publication: J Histochem Cytochem, 2010, Vol. 58, Page 221-8

PubMed ID: 19995946 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of preservation and protein extraction method on 2DE proteome analysis. Paraffin blocks of HOPE-fixed tissue were stored at 4 degrees C while formalin-fixed and ethanol-fixed paraffin-embedded tissue was stored at room temperature for an unspecified time prior to analysis.

   Summary of Findings:

   HOPE- and formalin-fixed specimens showed better preservation of morphological details than snap-frozen or ethanol-fixed specimens. The aqueous and complex methods of protein extraction yielded comparable 2DE spot patterns. Aqueous extraction of frozen specimens gave higher or lower protein yields, depending on the specimen, compared to aqueous extracted HOPE-fixed specimens. For complex protein extraction, higher yields and better reproducibility were observed for HOPE-fixed specimens compared to frozen specimens. Extraction of protein from formalin-fixed tissue with a specialized commercial kit resulted in fewer protein spots and lower resolution than aqueous extraction or complex extraction of HOPE-fixed and snap-frozen specimens. Protein yields were higher for frozen specimens than formalin-fixed specimens. 2DE results for ethanol-fixed specimens were superior to those for formalin-fixed specimens, but showed comparable spot patterns and inferior resolution and protein yields compared to HOPE-fixed specimens. The authors do not present a comparison of 2DE between ethanol-fixed specimens and frozen specimens.

   Biospecimens

   • Tissue - Lung

   Preservative Types

   • Formalin
   • Other Preservative
   • Frozen
   • Ethanol

   Diagnoses:

   • Normal
   • Neoplastic - Carcinoma
   • Neoplastic - Normal Adjacent

   Platform:

   Analyte	Technology Platform
   Protein	Colorimetric assay
   Protein	1D/2D gels
   Morphology	H-and-E microscopy

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) HOPE Ethanol Snap frozen
   Analyte Extraction and Purification	Analyte isolation method	Aqueous protein extraction Complex protein extraction QProteome FFPE Tissue 2D-PAGE kit

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