Pharmaceutical Sciences Faculty Publications

Document Type

Article

Publication Date

4-6-2012

Journal Title

Journal of Proteome Research

ISSN

1535-3907

Volume

11

Issue

4

First Page

2602

Last Page

2608

DOI

10.1021/pr201005t

PubMed ID

22352854

PubMed Central® ID

PMC3320745

Abstract

Formaldehyde-fixed, paraffin-embedded (FFPE) tissue repositories represent a valuable resource for the retrospective study of disease progression and response to therapy. However, the proteomic analysis of FFPE tissues has been hampered by formaldehyde-induced protein modifications, which reduce protein extraction efficiency and may lead to protein misidentification. Here, we demonstrate the use of heat augmented with high hydrostatic pressure (40,000 psi) as a novel method for the recovery of intact proteins from FFPE mouse liver. When FFPE mouse liver was extracted using heat and elevated pressure, there was a 4-fold increase in protein extraction efficiency, a 3-fold increase in the extraction of intact proteins, and up to a 30-fold increase in the number of nonredundant proteins identified by mass spectrometry, compared to matched tissue extracted with heat alone. More importantly, the number of nonredundant proteins identified in the FFPE tissue was nearly identical to that of matched fresh-frozen tissue.

Keywords

Hydrostatic pressure, liver, paraffin embedding, proteins, proteome, proteomics

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