Protein extraction studies formalin-fixed, paraffin-embedded

The sample materials from which proteins for proteomics studies may be extracted include fresh or snap-frozen cells from varied sources such as biological fluids, (serum, urine, plasma) and solid tissues such as biopsy specimens. Moreover, proteins isolated from ethanol-fixed paraffin-embedded tissues can be utilized for MS analysis.2 Protocols for the identification of proteins from formalin-fixed paraffin-embedded (FFPE) tissues have been recently developed.3 4 FFPE materials are the most common forms of biopsy archives utilized worldwide, and represent an important advancement for the large-scale interrogation of proteins in archival patient-derived materials. Finally, laser capture microdissected tissues have been successfully used for MS analysis.45... 

Frozen sections fixed in acetone have been a favored alternative to formalin-fixed, paraffin-embedded (FFPE) material in critical IHC work, to the point where this was considered the standard against which other fixatives were compared. Recent studies have now cast doubt on that status, showing that many antigens perform equally well after FFPE (with or without AR) and that nuclear antigens in particular fare better, perhaps because some proteins may be extracted by solvent fixatives. 

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